Portable, low-cost pathogen detection and strain identification platform

ABSTRACT

Methods for detecting the presence of a pathogen infection are described. In particular, this document provides a method of detecting target nucleic acids, such as pathogen-specific RNA, in a biological sample obtained from a subject, where the method comprises using one or more toehold switch sensors and an isothermal amplification step to detect the target nucleic acid. Methods specific for detecting and identify the presence of a virus such as Zika virus are also provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application represents the national stage entry of PCTInternational Application No. PCT/US2017/034545, filed on May 25, 2017,and claims the benefit of U.S. Provisional Patent Application No.62/341,221, filed on May 25, 2016, and U.S. Provisional PatentApplication No. 62/403,778, filed on Oct. 4, 2016, each of which isincorporated by reference it its entirety as if fully set forth herein.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

Not applicable.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on May 25, 2017, isnamed 112624_00851_SL.txt and is 217,680 bytes in size.

BACKGROUND

Synthetic biology is an emerging discipline that has great potential torespond to global pandemics. The increasing ability of syntheticbiologists to repurpose and engineer natural biological components forpractical applications has led to new opportunities for moleculardiagnostics.

In the case of viral outbreaks, standard serological approaches such asantibody detection have limited diagnostic value due to cross-reactivityin patients that have previously been infected by other flavivirusescirculating in the region. As a result, accurate diagnosis requiresnucleic acid-based detection methods, such as PCR and isothermal nucleicacid amplification. However, such techniques are expensive, requiretechnical expertise to run and interpret, and use equipment that isincompatible with use in remote and low-resource locations wheresurveillance and containment are critically needed. Accordingly, thereremains a need in the art for improved methods and devices for rapiddetection of target nucleic acids, including pathogen-specific nucleicacids for infection detection and for accurate strain identification.

BRIEF SUMMARY

In a first aspect, provided herein is a method of detecting a targetnucleic acid in a sample. In some cases, the method comprises orconsists essentially of the steps of: (a) obtaining nucleic acid from abiological sample obtained from a subject; (b) amplifying the nucleicacid using isothermal amplification; (c) contacting the amplifiednucleic acid to a toehold switch, wherein the toehold switch encodes areporter protein and comprises one or more single-stranded toeholdsequence domains that are complementary to a target nucleic acid or thereverse complement thereof, wherein the contacting occurs underconditions that allow translation of the coding domain in the presenceof the target nucleic acid but not in the absence of the target nucleicacid, and detecting the reporter protein as an indicator that the targetnucleic acid is present in the amplified nucleic acid of the subject;and (d) identifying the target nucleic acid as containing a targetprotospacer adjacent motif (PAM), wherein identifying comprises: (i)amplifying nucleic acid obtained from the biological sample using areverse primer designed to append the trigger sequence of one or moretoehold switch sequence domains; (ii) contacting the amplified nucleicacid of (i) to CRISPR/Cas under conditions that allow forsequence-specific cleavage of the contacted nucleic acid by CRISPR/Caswhen the target PAM is present in the amplified nucleic acid; and (iii)detecting activation of the toehold switch, wherein activation does notoccur in the event of CRISPR/Cas-mediated sequence-specific cleavage,thereby indicating the presence of the target PAM. The toehold switchcan comprise one or more single-stranded toehold sequence domains, afully or partially double-stranded stem domain comprising an initiationcodon, a loop domain comprising a ribosome binding site, and a codingdomain. The toehold and stem domains can be complementary in sequence toa naturally occurring RNA. The loop domain can be complementary insequence to a non-naturally occurring RNA. The target nucleic acid canbe an RNA specific to a pathogen. The pathogen is selected from thegroup consisting of a virus, bacterium, fungus, and parasite. In somecases, the pathogen is a virus. The virus can be Zika virus. The viruscan an American Zika variant (GenBank: KU312312). The virus strain canbe an African Zika variant (GenBank: KF268950). The toehold switch cancomprise an E. coli lacZ gene encoding β-galactosidase. Detectingactivation of the one or more toehold switch sensors can compriseperforming a LacZ-based colorimetric assay. Isothermal amplification canbe selected from the group consisting of NASBA (nucleic acidsequence-based amplification), loop-mediated isothermal amplification(LAMP), recombinase polymerase amplification (RPA), andhelicase-dependent amplification (HDA). The biological sample can beselected from the group consisting of blood, serum, urine, saliva,tissue, cell, and organ, or a fraction or portion thereof.

In another aspect, provided herein is a method of detecting a targetnucleic acid in a sample. In some cases, the method comprises orconsists essentially of: (a) obtaining RNA from a biological sampleobtained from a subject; (b) amplifying the RNA using isothermalamplification; (c) contacting the amplified RNA to a toehold switch,wherein the toehold switch encodes a reporter protein and comprises oneor more single-stranded toehold sequence domains that are complementaryto a target RNA or the reverse complement thereof, wherein thecontacting occurs under conditions that allow translation of the codingdomain in the presence of the target RNA but not in the absence of thetarget RNA, and detecting the reporter protein as an indicator that thetarget RNA is present in the amplified RNA of the subject; and (d)identifying the target RNA as containing a target protospacer adjacentmotif (PAM), wherein identifying comprises: (i) amplifying RNA obtainedfrom the biological sample using a reverse primer designed to append thetrigger sequence of one or more toehold switch sequence domains; (ii)contacting the amplified RNA of (i) to CRISPR/Cas under conditions thatallow for sequence-specific cleavage of the contacted RNA by CRISPR/Caswhen the target PAM is present in the amplified RNA; and (iii) detectingactivation of the toehold switch, wherein activation does not occur inthe event of CRISPR/Cas-mediated sequence-specific cleavage, therebyindicating the presence of the target nucleic acid. The toehold switchcan comprise one or more single-stranded toehold sequence domains, afully or partially double-stranded stem domain comprising an initiationcodon, a loop domain comprising a ribosome binding site, and a codingdomain. The toehold and stem domains can be complementary in sequence toa naturally occurring RNA. The loop domain can be complementary insequence to a non-naturally occurring RNA. The target nucleic acid canbe an RNA specific to a pathogen. The pathogen can be selected from thegroup consisting of a virus, bacterium, fungus, and parasite. In somecases, the pathogen is a virus. The virus can be Zika virus. The viruscan be an American Zika variant (GenBank: KU312312). The virus can be anAfrican Zika variant (GenBank: KF268950). The toehold switch cancomprise an E. coli lacZ gene encoding β-galactosidase. Detectingactivation of the one or more toehold switch sensors can compriseperforming a LacZ-based colorimetric assay. Isothermal amplification canbe selected from the group consisting of NASBA (nucleic acidsequence-based amplification), loop-mediated isothermal amplification(LAMP), recombinase polymerase amplification (RPA), andhelicase-dependent amplification (HDA). The biological sample isselected from the group consisting of blood, serum, urine, saliva,tissue, cell, and organ, or a fraction or portion thereof.

In a further aspect, provided herein is a method of detecting presenceof virus in a sample. The method can comprise or consist essentially ofthe steps of: (a) obtaining RNA from a biological sample obtained from asubject; (b) amplifying the RNA using isothermal amplification; (c)contacting the amplified RNA to a toehold switch, wherein the toeholdswitch encodes a reporter protein and comprises one or moresingle-stranded toehold sequence domains that are complementary to anendogenous virus RNA sequence or the reverse complement thereof, whereinthe contacting occurs under conditions that allow translation of thecoding domain in the presence of the endogenous virus RNA but not in theabsence of the endogenous virus RNA, and detecting the reporter proteinas an indicator that the endogenous virus RNA is present in theamplified RNA of the subject. The virus can be Zika virus. The toeholdswitch can comprise one or more Zika genome-specific single-strandedtoehold sequence domains, a thermodynamically stable double-strandedstem domain, a loop domain comprising a ribosome binding site, and acoding domain. The loop domain can be complementary in sequence to anaturally occurring RNA. The loop domain can be complementary insequence to a non-naturally occurring RNA. The loop domain can be 11nucleotides or 12 nucleotides. The toehold switch can comprise an E.coli lacZ gene encoding β-galactosidase. Isothermal amplification can beselected from the group consisting of NASBA (nucleic acid sequence-basedamplification), loop-mediated isothermal amplification (LAMP),recombinase polymerase amplification (RPA), and helicase-dependentamplification (HDA).

In another aspect, provided herein is a device for identifying apathogen, comprising a preserved paper test article, wherein a methodsdescribed herein is performed using the preserved paper test article.The paper test article can be preserved by freeze-drying.

In another aspect, provided herein is a kit for detecting a pathogen,comprising one or more of a device as described herein and an electronicoptical reader.

In a further aspect, provided herein is a method of genotyping a nucleicacid molecule. The method can comprise or consist essentially ofcontacting the nucleic acid molecule with: a programmable nuclease; anda sgRNA, wherein the combination of the nuclease and sgRNA canspecifically bind to at least one sequence variant of the nucleic acidmolecule; and detecting the presence or absence of a cut in the nucleicacid molecule generated by the nuclease. In some cases, the methodfurther comprises a first step of performing reverse transcription on aRNA molecule and performing 2nd strand DNA synthesis with a toeholdprimer to generate the nucleic acid molecule; and wherein the detectingstep comprises: transcribing an RNA from the nucleic acid molecule aftercontacting it with the nuclease, using a primer which initiatestranscription from a location distal of the sequence variation site withrespect to the location of the toehold primer sequence; and contacting asensor with the RNA resulting from step a) and detecting the presence orabsence of sensor activation; wherein the sensor is activated if thenuclease is not able to cut the nucleic acid molecule in step a). Thepresence of a cut can indicate that the nucleic acid molecule has asequence variant to which the sgRNA and nuclease can specifically bind.The presence of a cut can indicate that the nucleic acid molecule has asequence variant to which the nuclease specifically binds. Theprogrammable nuclease can be Cas. The sequence variant can occur at aPAM site. The nucleic acid molecule can be of human, animal,prokaryotic, eukaryotic, pathogenic, or synthetic origin. The nucleicacid molecule can be of viral origin. The viral nucleic acid moleculecan be a Zika virus nucleic acid molecule. The sequence variant beingdetected can differentiate at least one of the African, American, andAsian Zika strains from the others. The sequence variant can be selectedfrom Table 2. The sequence variant being detected can differentiate theAfrican and American Zika virus strains. The sequence variant can be theSNP occurring at site 7330 of the African (GenBank: KF268950) andAmerican (GenBank: KU312312) Zika strains. The sgRNA can have thesequence of SEQ ID NO: 1.

In another aspect, provided herein is a composition comprising a sgRNAwhich can specifically bind to a sequence flanking at least one sequencevariant selected from Table 2, wherein the sequence variation occurs ata CRISPR/Cas PAM binding site. The sgRNA can comprise SEQ ID NO: 1. ThesgRNA can be selected from Table 2.

In a further aspect, provided herein is a composition comprising aCRISPR/Cas nuclease and a sgRNA that specifically binds to a sequenceflanking at least one sequence variant occurring in a population. Thepopulation can be a viral population. The viral population can be a Zikavirus population. The variant can be selected from Table 2. The sgRNAcan be selected from Table 2. The sgRNA can comprise SEQ ID NO: 1.

These and other features, objects, and advantages of the presentinvention will become better understood from the description thatfollows. In the description, reference is made to the accompanyingdrawings, which form a part hereof and in which there is shown by way ofillustration, not limitation, embodiments of the invention. Thedescription of preferred embodiments is not intended to limit theinvention to cover all modifications, equivalents and alternatives.Reference should therefore be made to the claims recited herein forinterpreting the scope of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

The present invention will be better understood and features, aspects,and advantages other than those set forth above will become apparentwhen consideration is given to the following detailed descriptionthereof. Such detailed description makes reference to the followingdrawings, wherein:

FIG. 1 presents an exemplary workflow for rapid prototyping ofpaper-based, biomolecular sensors. Using sequence information fromonline databases, primers for isothermal RNA amplification and toeholdswitch-based RNA sensors were designed in silico using purpose-builtalgorithms. Once synthesized, the resulting sequence-specific toeholdsensors can be assembled and validated in less than 7 hours (hrs.). Inunder a day, validated sensors can be embedded into paper andfreeze-dried along with a cell-free transcription and translation systemto be deployed in the field as stable diagnostics. For the diagnostictest, extracted RNA is isothermally amplified via NASBA and used torehydrate the freeze-dried paper sensors. The detection of theappropriate trigger RNA is indicated by a color change in the paper discfrom yellow to purple.

FIGS. 2A-2D demonstrate rapid prototyping of 48 paper-based RNA toeholdsensors for Zika virus detection. (A) Series A toehold switch sensorschematic. The sensor design from Green et al., Cell 159:925-939 (2014)was modified with a shortened 11-nucleotide (nt) loop sequence to reduceleakage of output gene expression. (B) Series B toehold switch sensorschematic. Based on the same Zika genomic region as the A series, thesesensors include a 12-nt loop and lack the refolding domain. Thesemodifications were made to further reduce LacZ reporter leakage in theOFF state. (C) Maximum fold change in the rate of LacZ production forthe Series A Zika virus RNA sensors during the first 90 minutes (min) at37° C. Fold change of LacZ production rate is determined from the slopeof absorbance at 570 nm over time (sensor alone versus sensor with 3,000nM RNA trigger). Sensors are ordered according to fold change. (D)Maximum fold change in the rate of LacZ production for the Series B Zikavirus RNA sensors during the first 90 min at 37° C. Error bars representSD from three replicates. Inset: average LacZ absorbance of the OFFstates at 60 min indicates an overall reduction in LacZ reporter leakagefor the Series B sensors. Error bars represent SD across the 24 sensors.

FIGS. 3A-3C demonstrate detection of femtomolar (fM) concentrations ofZika virus RNA fragments. (A) Sensitivity of six of the best performingSeries A and B sensors without RNA amplification. Fold change iscalculated from absorbance (570 nm) after 30 minutes at 37° C. Errorbars represent SD from three replicates. (B) A schematic of NASBA(nucleic acid sequence based amplification)-mediated RNA amplification.(C) Zika RNA fragments diluted in water or 7% human serum were amplifiedusing NASBA with input concentrations ranging from 30 pM down to 3 fM. A1:7 dilution of the NASBA reaction in water was then used to rehydratefreeze-dried, paper-based reactions containing sensors 27B and 32B. Foldchange is calculated as described in (A) after 30 minutes at 37° C.

FIGS. 4A-4F demonstrate sensor specificity and sensitivity. (A) Linearresponse of sensors 27B, 31B and 32B to corresponding RNA trigger at 0nM, 3 nM, 30 nM and 300 nM. Each point represents the mean of triplicatedata taken at 60 min. (B) Orthogonality of sensors 27B, 7A and 32B totreatments of 3000 nM of trigger RNA from each of the three sensors. Theabsorbance output (570 nm) of the sensors at each time point wasconverted to a ratio of the maximum absorbance of respective sensor atthe 90 min time point and plotted as a heat map. Yellow indicates nosensor activation and purple indicates maximum sensor activation. (C)Reproducibility of NASBA reactions. Samples of Zika RNA in water or 7%human serum were amplified in three independent 2 hr. NASBA reactions.Each NASBA reaction was diluted 1:7 in water and used to rehydrate threefreeze-dried, paper-based reactions containing sensor 27B for a total ofnine replicates. Fold change was calculated from absorbance (570 nm)after 30 minutes at 37° C. Error bars represent SD from nine replicatesfor the 3 pM sample and three replicates for the 0 pM sample. (D) Effectof NASBA reaction time on sensitivity. Samples of Zika RNA in 7% humanserum were amplified in NASBA reactions for 30, 60, and 90 minutes.Diluted NASBA reactions (1:7) were tested with sensor 32B. Fold changewas calculated as above. Error bars represent SD of three replicates.(E) NASBA with freeze-dried reagents. Samples of Zika RNA in 7% humanserum were amplified by NASBA reagents in the standard formulation andby reagents freeze-dried in-house. Fold change and error bars werecalculated as above after 60 minutes. (F) Removing the 65° C. step fromNASBA protocol. Samples of Zika RNA in 7% human serum incubated at 95°C. for two minutes, mimicking viral lysis, and then amplified by NASBAaccording to the standard procedure without the 65° C. step. Fold changeand error bars were calculated as above after 60 minutes.

FIGS. 5A-5C present sequence alignments and RNA extraction optimizationdata. (A and B) Sequence alignments of Zika virus and Dengue virusgenomic regions targeted by sensors (A) 27B (SEQ ID NOS 777 and 778,respectively) and (B) 32B (SEQ ID NOS 779 and 780, respectively). Redboxes indicates sequences targeted by the respective toehold switches,red and blue boxes indicate the NASBA-amplified regions, and theremaining sequence indicates natural flanking RNA sequences from eachvirus. The entire Zika 32 sequence shown here was cloned into lentivirusto make proxy Zika virus. (C) Effect of boiling time on RNA extraction.Lentivirus was packaged with the Zika virus RNA fragment correspondingto sensor 32B. Virus was diluted to 10 and 3 fM target RNA in 7% humanserum. Twenty-five μL of virus was heated to 95° C. for 1 and 2 minutes.One μL was then used to initiate NASBA-mediated RNA amplification. A 1:7dilution of 2 hours NASBA reactions in water was then used to rehydratefreeze-dried, paper-based reactions. Fold change was calculated fromabsorbance (570 nm) after 60 minutes at 37° C. Error bars represent SDof three replicates.

FIGS. 6A-6D present data collected during development of a field-readydiagnostic platform. (A) Sequence specificity of Zika virus sensors 27Band 32B. Sensors were challenged with 3,000 nM of RNA corresponding totarget sequences from the Zika virus or the homologous region of theDengue virus. Fold change is calculated from absorbance (570 nm) at 60minutes after rehydration and incubation of freeze dried, paper-basedreactions at 37° C. Error bars represent SD from three replicates. (B)Zika virus sensors 27B and 32B were tested for specificity using NASBAreaction products derived from 300 fM input RNA corresponding to targetgenomic regions of the Zika or Dengue viruses in 7% human serum. Foldchange was calculated as in (A). (C) Using the portable electronicreader, time-course data were collected for Zika virus sensor 32B in thepresence of RNA amplified from 1 fM or 3 fM inputs of trigger RNA in 7%human serum. To increase sensitivity, NASBA reactions were run for 2.5hours. Graphs plot the relative absorbance of 570 nm wavelength lightcompared to background, which was collected every minute fromfreeze-dried, cell-free reactions embedded into paper. (D) Incorporatingviral sample processing into the diagnostic workflow. Lentivirus waspackaged with Zika RNA or homologous Dengue RNA fragments targeted bysensor 32B. Three femtomolar of virus was spiked into 7% human serum andheated to 95° C. for 2 minutes to extract viral RNA. The boiled lysatewas used to initiate NASBA-mediated RNA amplification. A 1:7 dilution ofthe 2 hours NASBA reaction in water was then used to rehydratefreeze-dried paper-based reactions. Time-course data were collected onthe portable electronic reader as in (C).

FIGS. 7A-7C present an exemplary portable electronic optical reader. (A)Line drawings used to cut the housing for the electronic reader fromblack acrylic using a laser cutter. (B) Image of the 16-reaction readerfrom the front. Chip containing paper-based sensors slides into the slotilluminated by the green light. Reader dimensions: 106 mm wide×116 mmdeep×96 mm high. (C) Components and circuit design used to assemble theelectronic optical reader.

FIGS. 8A-8E illustrate an exemplary protocol for strain differentiationat single-base resolution. (A) Schematic representation of NASBA-CRISPRCleavage (NASBACC)-genotyping following a positive Zika diagnosis. Asynthetic trigger sequence is appended to a NASBA-amplified RNA fragmentthrough reverse transcription. The presence of a strain-specific PAMleads to the production of either truncated or full-length trigger RNA,which differentially activates a toehold switch (sensor H) (Pardee etal., 2014). (B) The probability that a non-biased single nucleotidepolymorphism (SNP) between two strains can be discriminated byCRISPR/Cas9 is 48% (Table S4). Hence, genetic drift between the Americanand African or Asian strains, while relatively small (14.4% and 4.9%sequence dissimilarity, respectively), has created hundreds ofstrain-specific PAM sites. (C) A SNP between African (GenBank: KF268950)and American (GenBank: KU312312) strains at site 7330 (SEQ ID NOS 782and 781, respectively) disrupts an existing PAM site, allowing forCas9-mediated DNA cleavage only in the American strain. (D) Sensor 32Bcan distinguish between Dengue and Zika RNA sequences but cannotdiscriminate between American and African Zika strains. Paper discscontaining sensor 32B were rehydrated with 300 nM trigger RNAcorresponding to sequences from American-Zika, African-Zika, or Dengue.Colorimetric outputs: a purple color indicates the activation of LacZexpression from the toehold switch, and a yellow color indicates thetoehold switch remained inactive. (E) NASBACC can discriminate betweenAmerican- and African-lineages of Zika virus. Paper discs containingsensor H were rehydrated with a 1:10 dilution of NASBACC reactionsinitiated with 0.05 μl of a 300 nM RNA sample. In this case, an inactivetoehold switch leads to a positive identification of the American Zikastrain.

FIGS. 9A-9B present data from a CRISPR nuclease assay using fresh andfreeze-dried reactions. (A) Sequence information and location of thegRNA used to target the lacZ gene (SEQ ID NOS 783-788, respectively, inorder of appearance). Each sequence was selected for maximum activityusing the Doench et al. scoring algorithm (Doench et al., 2014). (B) Gelshowing the length of supercoiled versus cut DNA following the in vitrodigestion of a lacZ-containing plasmid for fresh and freeze-driedreactions. Note that the activity of some gRNA/Cas9 combinations isimproved under freeze-dried conditions.

FIGS. 10A-10D are graphs data from assays validating diagnostic workflowon live Zika virus samples. (A) Specificity of sensor 32B againstpurified genomic RNA. Sensor 32B was tested for specificity using NASBAreaction products performed on 30 fM RNA purified from Zika virus andthree different Dengue virus serotypes. Fold change is calculated fromabsorbance (570 nm) at 60 minutes (min) after rehydration and incubationof freeze-dried, paper-based reactions at 37° C. Error bars represent SDfrom three replicates. (B) Detection of live Zika virus. Ten femtomolar(fM) of laboratory-cultured Zika virus was spiked into human serum (7%),heated to 95° C. for 2 min, and used to initiate NASBA-mediated RNAamplification. A 1:7 dilution of the 3 hour (hr.) NASBA reaction inwater was then used to rehydrate freeze-dried, paper-based reactions.Time-course data were collected on the portable electronic reader. Graphplots the relative absorbance of 570 nm wavelength light compared tobackground. Error bars represent SD from three replicates. (C and D)Detection of Zika virus in viremic rhesus macaque plasma using sensors27B and 32B. Plasma containing 2.8 fM of Zika virus was diluted 1:10 innuclease free water, heated to 95° C. for 2 minutes, and used toinitiate NASBA-mediated RNA amplification. 3 hr. NASBA reactions weremonitored on the portable electronic reader as in (B).

FIG. 11 depicts a schematic of NASBA-CRISPR Cleavage (NASBACC).

FIG. 12 demonstrates that Cas9 without guide RNA does not interfere withNASBA.

FIG. 13 demonstrates that Cas9 with a gRNA targeting a site lacking aPAM site does not interfere with NASBA.

FIG. 14 depicts a graph of the effect of primer concentration onNASBACC.

While the present invention is susceptible to various modifications andalternative forms, exemplary embodiments thereof are shown by way ofexample in the drawings and are herein described in detail. It should beunderstood, however, that the description of exemplary embodiments isnot intended to limit the invention to the particular forms disclosed,but on the contrary, the intention is to cover all modifications,equivalents and alternatives falling within the spirit and scope of theinvention as defined by the appended claims.

DETAILED DESCRIPTION

All publications, including but not limited to patents and patentapplications, cited in this specification are herein incorporated byreference as though set forth in their entirety in the presentapplication.

The methods and compositions provided herein are based at least in parton the Inventors' development of a diagnostic platform utilizingengineered biomolecular, nucleic acid-based sensors and CRISPR-basedtechnology that permits rapid, specific, and low-cost detection of viralnucleic acids at clinically relevant concentrations. In particular, theinventors developed engineered biomolecular sensors for the specificdetection of pathogen genomes such as viral RNA genomes.

Without being bound to any particular theory or mechanism of action, itis believed that the inventors addressed limitations in the practicaldeployment of nucleic acid-based molecular diagnostics by combiningisothermal RNA amplification with toehold switch sensors on afreeze-dried, paper-based platform. By automating the amplificationprimer and sensor design process using in silico algorithms, the methodsdescribed herein provide clinically relevant sensitivity, discriminatingbetween pathogen genotypes with single-base resolution.

Accordingly, in a first aspect, provided herein is a method of detectinga target nucleic acid in a biological sample obtained from a subject. Asdescribed herein, the method comprises or consists essentially of (a)obtaining nucleic acid (e.g., DNA, RNA) from a biological samplecontaining or suspected of containing a target nucleotide sequence; (b)amplifying the nucleic acid using a primer designed to hybridize to thetarget nucleotide sequence; (c) contacting the amplified nucleic acid toa toehold switch, where the riboregulator encodes a reporter protein andcomprises one or more toehold sequence domains that are complementary tothe target nucleotide sequence, where the contacting occurs underconditions that allow translation of the coding domain in the presenceof the target nucleic acid but not in the absence of the target nucleicacid, and detecting the reporter protein as an indicator that the targetnucleic acid is present in the amplified nucleic acid of the subject.

In certain embodiments, the target nucleotide sequence is a nucleic acidfrom a pathogen, where the biological sample contains or is suspected ofcontaining the pathogen. Accordingly, the methods provided herein areuseful to detect any pathogen or infectious agent. Pathogens andinfectious agents may comprise viruses, (e.g., single stranded RNAviruses, single stranded DNA viruses, Zika virus, HIV, hepatitis A, B,and C virus, HSV, CMV EBV, HPV), parasites (e.g., protozoan and metazoanpathogens such as Plasmodia species, Leishmania species, Schistosomaspecies, Trypanosoma species), bacteria (e.g., Mycobacteria, inparticular, M. tuberculosis, Salmonella, Streptococci, E. coli,Staphylococci), fungi (e.g., Candida species, Aspergillus species),Pneumocystis carinii, and prions. In certain embodiments, the pathogenis a virus, and the methods can be used to detect any virus. In otherembodiments, the pathogens that are detected are bacteria, fungi, orparasites. An advantage of the methods and systems described herein isthat they can be applied for the detection and identification ofessentially any nucleic acid-containing organism. Accordingly, thepathogen or infectious agent can be virtually any pathogen or infectiousagent for which genetic information (e.g., gene sequences) is available.In other cases, the target nucleic acid is human in origin. In suchcases, the methods can be employed to detect one or more target nucleicacids in a biological sample such as a biological sample obtained forforensic analysis, for genotyping, and the like.

In such cases, the methods provided herein can further compriseidentifying the pathogen detected in the biological sample. For example,the method can further comprise (i) amplifying RNA obtained from thebiological sample; (ii) contacting the amplified RNA of (i) to anuclease under conditions that allow for sequence-specific cleavage ofthe contacted RNA by the nuclease when a pathogen strain-specificprotospacer adjacent motif (PAM) is present; and (iii) detectingactivation of a toehold switch, where activation does not occur in theevent of nuclease-mediated sequence-specific cleavage, therebyindicating the presence of the pathogen strain-specific PAM. In othercases, DNA is obtained from the biological sample and amplified asdescribed above.

Other target nucleotide sequences include, without limitation, DNA orRNA sequences that can identify a species (e.g., ribosomal RNAs orDNAs); DNA or RNA sequences that are associated with a particulargenetic condition (e.g., where the target comprises a single nucleotidepolymorphism (SNP) for which PAM identification is advantageous,including, without limitation, BRCA1/BRCA2 mutations, cystic fibrosis,Duchenne muscular dystrophy, hemochromatosis); DNA or RNA sequences foridentifying a particular person with high certainty (e.g., identifying asuspect in a criminal investigation; identifying a “high value target”in a military operation).

For forensic applications, the target nucleotide sequence can be a DNAor RNA sequence associated with one or more particular identifiablefeatures (e.g., skin color, hair color, eye color). In such cases, abiological sample can be assayed to detect a target nucleic acid of anunknown subject or for comparison to samples from known individuals. Forapplications related to pathogen detection, detection of particular RNAsequences is advantageous for determining, for example, the life cyclestage of a pathogen associated with an infection. By way of example,particular target nucleic acids can be detected to detect the presenceof malaria parasite Plasmodium falciparum and to determine whether theparasite is in a life cycle phase in which it can reproduce and, thus,transmit infection. Other applications for which the methods providedherein include, without limitation, profiling species in an environment(e.g., water); profiling species in an human or animal microbiome; foodsafety applications (e.g., detecting the presence of a pathogenicspecies, determining or confirming food source/origin such as type ofanimal or crop plant); obtaining patient expression profiles (e.g.,detecting expression of a gene or panel of genes (e.g., biomarkers) tomonitor the patient's response to a therapeutic regimen, to select atherapeutic regimen suitable for the patient, or to detect exposure ofthe patient to a toxin or environmental agent that affects expression ofthe gene or panel of genes; and molecular encryption applications suchas marking certain products (e.g., high value products) using nucleicacid barcodes.

The nucleic acid molecule can be, e.g., an RNA, a DNA, an mRNA, and/or agenomic nucleic acid. In some embodiments of any of the aspects, thenucleic acid molecule can be human, animal, prokaryotic, eukaryotic, orpathogenic in origin. In some embodiments of any of the aspects, thenucleic acid molecule can be of viral origin. Nucleic acids and/or othermoieties of the invention may be isolated. As used herein, “isolated”means separate from at least some of the components with which it isusually associated whether it is derived from a naturally occurringsource or made synthetically, in whole or in part.

Nucleic acids and/or other moieties of the invention may be purified. Asused herein, purified means separate from the majority of othercompounds or entities. A compound or moiety may be partially purified orsubstantially purified. Purity may be denoted by a weight by weightmeasure and may be determined using a variety of analytical techniquessuch as but not limited to mass spectrometry, HPLC, etc.

Biological samples appropriate for use according to the methods providedherein include, without limitation, blood, serum, urine, saliva,tissues, cells, and organs, or portions thereof.

Since the methods of the present invention provide single-basediscrimination, the methods are particularly suited to distinguishingbetween genomes of a pathogen strain (e.g., to distinguish betweenpathogen strains) and/or identifying the presence of nucleic acidsspecific to a particular pathogen. As described herein, the methodsincorporate isothermal RNA amplification and the sequence-specificnuclease activity of a CRISPR/Cas system. “Clustered RegularlyInterspaced Palindromic Repeats (CRISPRs)/CRISPR associated (Cas)”systems have been employed for targeted genome editing applicationsacross many species. CRISPR systems belong to different classes, withdifferent repeat patterns, sets of genes, and species ranges. The numberof Cas genes at a given CRISPR locus can vary between species. The terms“Cas gene” and “CRISPR-associated (Cas) gene” are used interchangeablyherein. A comprehensive review of the Cas protein family is presented inHaft et al. (2005) Computational Biology, PLoS Comput. Biol. 1:e60(doi:10.1371/journal.pcbi.0010060). At least 41 CRISPR-associated (Cas)gene families have been described.

Without being bound to any particular theory or mechanism of action, Casenzymes recognize a strain-specific protospacer adjacent motif (PAM)sequence. In one embodiment, in the case of the enzyme Cas9 the PAMsequence is NGG, where N can be any DNA base. Thus, a single basemutation, such as one that changes the sequence AGG to AAG, abolishesthe PAM site and prevents Cas nuclease-based cleavage. As used herein,the term “protospacer” refers to the portion of a crRNA (or sgRNA) thatis complementary to the genomic DNA target sequence. Generally,protospacers are usually 20 nucleotides in length. Referring to FIG. 8,the methods provided herein can employ pathogen strain-specific “NGG”protospacer adjacent motif (PAM) sequences and isothermal RNAamplification using primers having specificity to the toehold switchdomain. In such cases, the amplified DNA will undergo Cas-mediatedcleavage only if the appropriate strain-specific PAM sequence ispresent. The truncated RNA, generated through transcription of thecleaved DNA product, is unable to activate the toehold switch. In theabsence of the PAM sequence, the full-length RNA product containing thetoehold switch domain is generated, allowing for nucleic acid-basedsensor activation. Trigger RNA is only amplified from DNA that is notcut by Cas, thereby allowing for strain-specific detection using thetoehold switch. With respect to distinguishing between Zika virusstrains, analysis of the sequences of the American Zika variant(GenBank: KU312312) and an African Zika variant (GenBank: KF268950)revealed over 600 sites at which a PAM site was present in one strainand not the other. Since both viruses have genomes of ˜10.5 kb inlength, PAM sites that can be used to identify viruses in astrain-specific manner occur approximately every 17 bases within thegenomes of the two closely related strains and thus provide considerableopportunities for strain identification according to the methodsprovided herein.

As used herein, the term “toehold switch” generally refers to a nucleicacid-based regulator of gene expression, configured to repress oractivate translation of an open reading frame and thus production of aprotein. Toehold switches, which are a type of prokaryoticriboregulator, activate gene expression in response to cognate RNAs withessentially arbitrary sequences. Gene regulation is achieved through thepresence of a regulatory nucleic acid element (the cis-repressive RNA orcrRNA) within the 5′ untranslated region (5′ UTR) of an mRNA molecule.The cis-repressive nucleic acid element (crRNA) forms a hairpinstructure comprising a stem domain and a loop domain throughcomplementary base pairing. The hairpin structure blocks access to themRNA transcript by the ribosome, thereby preventing translation. In someembodiments, the stem domain of the hairpin structure sequesters theribosome binding site (RBS). In some embodiments, including for exampleembodiments involving eukaryotic cells, the stem domain of the hairpinstructure is positioned upstream of the start (or initiation) codon,within the 5′ UTR of an mRNA. In some cases, riboregulators comprisesynthetic (engineered) molecules. In other cases, toehold switchescomprise endogenous, naturally occurring RNAs or regions thereof. See,for example, U.S. 2015/0275203. The stem domain can be as small as 12bps, but in some cases will be longer than 12 bps, including 13, 14, 15,16, 17, 18, 19, 20, or more base pairs in length. In some cases, theloop domain is complementary to a naturally occurring RNA. In othercases, the loop domain is complementary to a non-naturally occurringRNA. The toehold domain can be 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, or more nucleotides in length. Referring to FIGS. 2Aand 2B, an exemplary toehold switch domain comprises an 11-nt or 12-ntloop domain.

The toehold switch further comprises a fully or partiallydouble-stranded stem domain comprising an initiation codon, a loopdomain comprising a ribosome binding site (RBS), and a coding domain.The unpaired region upstream of the RBS in a toehold switch can beshortened or lengthened to modulate protein output and, in turn, devicedynamic range. In some cases, the toehold and stem domains arecomplementary in sequence to a naturally occurring RNA. In other cases,the sequence detected can also be the complement of the naturallyoccurring RNA. For example, after isothermal amplification, it ispossible to transcribe the antisense of the RNA rather than the sense.

The toehold switch can further comprise a thermodynamically stabledouble-stranded stem domain, a loop domain comprising a ribosome bindingsite, and a coding domain. In some cases, the loop domain iscomplementary in sequence to a naturally occurring Zika virus RNA. Inother cases, the loop domain is complementary in sequence to anon-naturally occurring RNA. Preferably, the loop domain is 11nucleotides or 12 nucleotides in length. In some cases, the length ofloop domains can be increased or decreased, for example, to alterreaction thermodynamics.

As shown in FIGS. 2A and 2B, the toehold switch can be operably linkedto a reporter element (e.g., an E. coli lacZ reporter element encodingβ-galactosidase) that is 3′ to the hairpin structure. As used herein,the term “operably linked” refers to a relationship between two nucleicacid sequences wherein the production or expression of one of thenucleic acid sequences is controlled by, regulated by, modulated by,etc., the other nucleic acid sequence. Reporter proteins appropriate forthe methods provided herein include, without limitation, enzymaticreporters (e.g., β-galactosidase, alkaline phosphatase, DHFR, CAT),fluorescent or chemiluminescent reporters (e.g., GFP variants, mCherry,luciferase, e.g., luciferase derived from the firefly (Photinus pyralis)or the sea pansy (Renilla reniformis) and mutants thereof), etc.

Any isothermal amplification protocol can be used according to themethods provided herein. Exemplary types of isothermal amplificationinclude, without limitation, nucleic acid sequence-based amplification(NASBA), loop-mediated isothermal amplification (LAMP), stranddisplacement amplification (SDA), helicase-dependent amplification(HDA), nicking enzyme amplification reaction (NEAR), signal mediatedamplification of RNA technology (SMART), rolling circle amplification(RCA), isothermal multiple displacement amplification (IMDA), singleprimer isothermal amplification (SPIA), recombinase polymeraseamplification (RPA), and polymerase spiral reaction (PSR available atnature.com/articles/srep12723 on the World Wide Web). In some cases, aforward primer is used to introduce a T7 promoter site into theresulting DNA template to enable transcription of amplified RNA productsvia T7 RNA polymerase. In other cases, a reverse primer is used to add atrigger sequence of a toehold sequence domain.

As used herein, “nuclease” refers to an enzyme capable of cleaving thephosphodiester bonds between the nucleotide subunits of nucleic acids.Nucleases can be site-specific, i.e. site-specific nucleases cleave DNAbonds only after specifically binding to a particular sequence.Therefore, nucleases specific for a given target can be readily selectedby one of skill in the art. Nucleases often cleave both strands of dsDNAmolecule within several bases of each other, resulting in adouble-stranded break (DSB). Exemplary nucleases include, but are notlimited to Cas9; Cas13; meganucleases; TALENs; zinc finger nucleases;FokI cleavage domain; RNA-guided engineered nucleases; Cas-derivednucleases; homing endonucleases (e.g. I-AniI, I-CreI, and I-SceI) andthe like. In some embodiments of any of the aspects, the nuclease is anendonuclease. As used herein, “endonuclease” refers to an enzyme capableof cleaving the phosphodiester bonds between the nucleotide subunits ofnucleic acids within a polynucleotide, e.g., cleaving a phosphodiesterbond that is not either the 5′ or 3′ most bond present in thepolynucleotide. In other embodiments of any of the aspects, the nucleaseis a meganuclease. As used herein, “meganuclease” refers toendonucleases, which have a large recognition sequence (e.g., dsDNAsequences of 12-40 bp). Due to the size of the recognition sequences,meganucleases are particularly specific. Meganuclease specificity can beengineered. In some embodiments of any of the aspects, the meganucleasecan be a LAGLIDADG homing endonuclease (SEQ ID NO: 2).

In some embodiments, the nuclease can be an engineered nuclease. As usedherein, the terms “engineered” and “genetically engineered” are usedinterchangeably and refer to the aspect of having been manipulated bythe hand of man. For example, a nuclease is considered to be“engineered” when the sequence of the nuclease is manipulated by thehand of man to differ from the sequence of the nuclease as it exists innature. As is common practice and is understood by those in the art,progeny and copies of an engineered polynucleotide and/or polypeptideare typically still referred to as “engineered” even though the actualmanipulation was performed on a prior entity. Methods of engineeringnucleases to achieve a desired sequence specificity are known in the artand are described, e.g., in Kim and Kim. Nature Reviews Genetics 201415:321-334; Kim et al. Genome Res. 2012 22:1327-1333; Belhaj et al.Plant Methods 2013 9:39; Urnov et al. Nat Rev Genet 2010 11:636-646;Bogdanove et al. Science 2011 333:1843-6; Jinek et al. Science 2012337:816-821; Silva et al. Curr Gene Ther 2011 11:11-27; Ran et al. Cell2013 154:1380-9; Carlson et al. PNAS 212 109:17382-7, Guerts et al.Science 2009 325:433-3; Takasu et al. Insect Biochem Mol Biol 201040:759-765; and Watanabe et al. Nat. Commun. 2012 3; each of which isincorporated by reference herein in its entirety.

In some embodiments, the nuclease is a programmable nuclease. As usedherein “programmable nuclease” refers to a nuclease that has beenengineered to create a double-stranded break (DSB) or nick at a nucleicacid sequence that the native nuclease would not act upon, e.g. thesequence specificity of the nuclease has been altered. As describedherein, programmable nucleases can be used to genotype a nucleic acidand/or determine the sequence of a nucleic acid. In particular,programmable nucleases can differentiate between point mutations orSNPs, e.g., SNPs that occur in a PAM site. In one aspect of any of theembodiments, described herein is a method of genotyping a nucleic acidmolecule, the method comprising: a) contacting the nucleic acid moleculewith: a programmable nuclease; and a single guide (“sgRNA”) which canspecifically bind to at least one sequence variant of the nucleic acidmolecule; and b) detecting the presence or absence of a cut in thenucleic acid molecule generated by the nuclease. In one aspect of any ofthe embodiments, described herein is a method of genotyping a nucleicacid molecule, the method comprising: a) contacting the nucleic acidmolecule with: a programmable nuclease; and a sgRNA wherein thecombination of the nuclease and sgRNA can specifically bind to at leastone sequence variant of the nucleic acid molecule; and b) detecting thepresence or absence of a cut in the nucleic acid molecule generated bythe nuclease. In some embodiments of any of the aspects, the presence ofa cut indicates that the nucleic acid molecule has a sequence variantfor which the sgRNA is specific. In some embodiments of any of theaspects, the presence of a cut indicates that the nucleic acid moleculehas a sequence variant to which the nuclease specifically binds. In someembodiments of any of the aspects, the presence of a cut indicates thatthe nucleic acid molecule has a sequence variant for which the sgRNA isspecific and has a sequence variant to which the nuclease specificallybinds. In some embodiments of any of the aspects, the presence of a cutindicates that the nucleic acid molecule has a sequence variant to whichthe sgRNA and nuclease can specifically bind.

By way of non-limiting example, the programmable nuclease can be Cas9;Cas13, a Cas nickase mutant; TALEN; ZFNs; Cpf1; and/or SaCas9. In someembodiments of any of the aspects, the programmable nuclease is Cas9. Insome embodiments, the programmable nuclease is Cas9. In some embodimentsof any of the aspects, the programmable nuclease is S. pyogenes Cas9 ora variant thereof, e.g., New England Biolabs #M0386 (Ipswich, Mass.).When Cas9 nuclease (or Cas9-derived nuclease) is selected for use, thenuclease will generate a cut and/or nick where the guide RNA hybridizesto the nucleic acid molecule.

In order for a Cas nuclease to recognize and cleave a target nucleicacid molecule, a CRISPR targeting RNA (“crRNA”) and trans-activatingcrRNA (“tracrRNA”) must be present. crRNAs hybridize with tracrRNA toform a hybrid guide RNA (“gRNA”) which then associates with the Cas9nuclease. Alternatively, the gRNA can be provided as a single contiguousRNA, and forms a single guide RNA (“sgRNA”). Once the sgRNA is complexedwith Cas, the complex can bind to a target nucleic acid molecule. ThesgRNA binds specifically to a complementary target sequence via atarget-specific sequence in the crRNA portion (e.g., the spacersequence), while Cas itself binds to a protospacer adjacent motif(CRISPR/Cas protospacer-adjacent motif; PAM). The Cas nuclease thenmediates cleavage of the target nucleic acid to create a double-strandedbreak within the sequence bound by the sgRNA. Different Cas enzymes havedifferent PAM recognition sequences. For example, S. pyogenes Cas9requires a NGG PAM sequence while other CRISPR/Cas systems have beendescribed in other prokaryotic species, which recognize a different PAMsequence (e.g., CCN, TCN, TTC, AWG, CC, NNAGNN, NGG, NGGNG).

In some embodiments of any of the aspects, the sgRNA is provided as asingle continuous nucleic acid molecule. In some embodiments of any ofthe aspects, a hybrid gRNA is provided as a set of hybridized molecules,e.g., a crRNA and tracrRNA.

In embodiments in which the nuclease to which the amplified DNA or RNAis contacted is a Cas nuclease, a method of detecting a viral nucleicacid comprises or consists essentially of: (a) obtaining DNA or RNA froma biological sample obtained from a subject; (b) amplifying the DNA orRNA using a primer designed to append a trigger sequence of one or moretoehold sequence domains; (c) contacting the amplified DNA or RNA to atoehold switch, where the riboregulator encodes a reporter protein andcomprises one or more toehold sequence domains, where the contactingoccurs under conditions that allow translation of the coding domain inthe presence of the endogenous virus DNA or RNA but not in the absenceof the endogenous virus DNA or RNA, and detecting the reporter proteinas an indicator that the endogenous virus DNA or RNA is present in theamplified DNA or RNA of the subject; and (d) identifying the strain ofvirus, where identifying comprises: (i) amplifying DNA or RNA from thebiological sample; (ii) contacting the amplified DNA or RNA of (i) toCas (e.g., Cas9, Cas13) under conditions that allow forsequence-specific cleavage of the contacted RNA by Cas (e.g., Cas9,Cas13) when a virus strain-specific protospacer adjacent motif (PAM) ispresent; and (iii) detecting activation of the toehold switch, whereactivation does not occur in the event of Cas-mediated sequence-specificcleavage, thereby indicating the presence of the virus strain-specificPAM. For example, the methods provided herein can be used to distinguishbetween viral strains, e.g., where one strain comprises a PAM site whilethe second strain comprises a SNP that eliminates the PAM site, such anAmerican Zika variant (GenBank: KU312312) and an African Zika variant(GenBank: KF268950), and also between other flavivirus strains. See,FIGS. 5A-5B. In such cases the toehold switch comprises one or more Zikagenome-specific single-stranded toehold sequence domains. Exemplarysequences of toehold switches suitable for use for Zika RNA detectionare provided in Table 8.

In some cases, the one or more toehold sequence domains arecomplementary to an endogenous virus DNA or RNA sequence. In such cases,where the toehold switch recognizes an endogenous RNA sequence, there isno requirement for a primer that appends a toehold sequence domain.

With respect to the amplification step, the target sequence for atoehold switch is in some cases added via an amplification primer forthe NASBACC process. In other cases, a toehold switch that detects anendogenous pathogen DNA or RNA sequence is used.

In another aspect, provided herein is a method of detecting Zika virusin a sample. The methods can comprises, or consist essentially of, (a)obtaining RNA from a biological sample obtained from a subject; (b)amplifying the RNA using isothermal amplification; and (c) contactingthe amplified RNA to a riboregulator, wherein the riboregulator encodesa reporter protein and comprises one or more toehold domains that iscomplementary to a Zika virus RNA, wherein the contacting occurs underconditions that allow translation of the coding domain in the presenceof the Zika virus RNA but not in the absence of the Zika virus RNA, anddetecting the reporter protein as an indicator that the Zika virus RNAis present in the amplified RNA of the subject.

In some cases, it may be advantageous to adapt the methods describedherein for high-throughput, reproducible, and rapid detection, forexample in a clinical setting. When riboregulator output is coupled to areporter element, such as a LacZ reporter element, the riboregulatoracts as a genetically encodable sensor and detectable probe forendogenous DNA or RNA (e.g., endogenous pathogen DNA, endogenouspathogen RNA) in a sample. For example, such toehold switches can beprovided in a device configured for rapid, reproducible detection in aclinical setting. In some cases, the device comprises a preserved papertest article, upon which any step(s) of the method provided herein canbe performed. In preferred embodiments, the paper test article ispreserved by freeze-drying. The reporter element can be a reporterprotein, e.g., a polypeptide with an easily assayed enzymatic activityor detectable signal that is naturally absent from the host cell.Exemplary but non-limiting reporter proteins include lacZ, catalase,xy1E, GFP, RFP, YFP, CFP, neomycin phosphotransferase, luciferase,mCherry, and derivatives or variants thereof. In some embodiments of anyof the aspects, the reporter protein is suitable for use in acolorimetric assay. Examples of genes encoding fluorescent proteins thatmay be used in accordance with the invention include, withoutlimitation, those proteins provided in U.S. Patent Application No.2012/0003630 (see Table 59 therein), incorporated herein by reference.

In some cases, the device is used with a portable electronic reader. Inthis manner, the electronic reader serves as companion technology thatprovides robust and quantitative measurements of device outputs. Asshown in FIGS. 7A-7C, an exemplary electronic reader comprises readilyavailable consumer components, open-source code, and laser-cut acrylichousing, and is powered by a rechargeable lithium ion battery. Theelectronic reader can further comprise an onboard data storage unit. Insome cases, to achieve sensitive detection of toehold switch signaloutput, an acrylic chip that holds the freeze-dried, paper-basedreactions is placed into the reader between an LED light source (570 nm)and electronic sensors. Using onboard electronics, samples can be readat a rate of 29 reads per minute. Accordingly, the portable electronicreader provides low-noise measurements of changes associated with thereporter element including changes in light transmission due toLacZ-mediated color change.

As used herein, “sequence variations” can refer to substitutions,insertions, deletions, duplications, and/or rearrangements. Sequencevariations of a locus occurring in a population are referred to asalleles. Sequence variations can be present in (and therefore, detectedin) the gDNA and/or mRNA of a gene. In some embodiments of any of theaspects, the sequence variation is a point mutation, e.g. a singlenucleotide polymorphism (SNP). As used herein, a “point mutation” refersto the identity of the nucleotide present at a site of a mutation in themutant copy of a genomic locus (including insertions and deletions),i.e., it refers to an alteration in the sequence of a nucleotide at asingle base position from the wild type sequence. A SNP (singlenucleotide polymorphism) is one type of point mutation that occurs atthe same genomic locus between different individual subjects or entitiesin a population or different strains in a species. SNPs can be allelic.At least four alleles of a SNP locus are possible, although SNPs thatvary only between two nucleotides at the target site are not uncommon.

In some embodiments of any of the aspects, the target nucleic acid is aZika virus nucleic acid molecule, e.g., a Zika virus genomic molecule ora molecule transcribed from the Zika virus genome.

The methods described herein can permit identification of the species ofvirus present in a sample (e.g., a sample obtained from a subject),and/or permit identification of the strain of a virus present in asample based upon sequence variations found between species and/orstrains. Such information can be used to direct treatment, e.g.,different strains of Zika virus are known to cause different symptomsand secondary conditions at varying frequencies. In some embodiments ofany of the aspects, the sequence variant being detected differentiatesat least one of the African, American, and Asian Zika strains from theothers. Exemplary sequence variants that differentiate these strains areprovided in Table 5.

In certain embodiments, provided herein is a method for genotyping anucleic acid molecule. The method can comprise or consist essentially ofcontacting the nucleic acid molecule with a programmable nuclease and asgRNA, where the combination of the nuclease and sgRNA can specificallybind to at least one sequence variant of the nucleic acid molecule; anddetecting the presence or absence of a cut in the nucleic acid moleculegenerated by the nuclease. In some cases, the method further comprises afirst step of performing reverse transcription on a RNA molecule andperforming 2nd strand DNA synthesis with a toehold primer to generatethe nucleic acid molecule. In such cases, the detecting step comprises:(i) transcribing an RNA from the nucleic acid molecule after contactingit with the nuclease, using a primer which initiates transcription froma location distal of the sequence variation site with respect to thelocation of the toehold primer sequence; and (ii) contacting a sensorwith the RNA resulting from step (a) and detecting the presence orabsence of sensor activation; wherein the sensor is activated if thenuclease is not able to cut the nucleic acid molecule in step (a). Asused herein, the term “toehold primer” refers to an oligonucleotideprimer configured to add a detectable tag or label sequence, where thetag or label sequence is detectable by a downstream nucleic acid sensor.

Primers and sgRNAs can readily be designed for a given variant accordingto the principles described herein. Cas9 selectively cleaves DNA only inthe presence of an NGG protospacer adjacent motif (PAM). As demonstratedherein, e.g. in Example 1, numerous strain-specific PAM sites exist. Thereverse transcription primer is designed to specifically bind near theselected PAM site such that reverse transcription proceeds towards thePAM site. The sgRNA and/or guide RNA is then designed to specificallybind to a sequence located between the PAM site and the sequence towhich the reverse transcription primer specifically binds. Tools fordesigning primers and sgRNAs are known in the art. For example, a primersequence can be selected to have a desired T_(M) (melting temperature)using any of a number of widely available algorithms (e.g., OLIGO™(Molecular Biology Insights Inc. Colorado) primer design software andVENTRO NTI™ (Invitrogen, Inc. California) primer design software andprograms available on the internet, including Primer3 and OligoCalculator). Algorithms are also widely available for sgRNA design(e.g., several online tools (e.g., The Broad Institute's sgRNA Designtool, CRISPR Design or CHOPCHOP, which are available on the internet).Methods of making primers and other nucleic acid sequences (e.g.,oligonucleotides, sgRNAs) are well known in the art, and numerouscommercial sources offer oligonucleotide synthesis services suitable forproviding molecules according to the methods and compositions describedherein, e.g. INVITROGEN™ Custom DNA Oligos; Life Technologies; GrandIsland, N.Y. or custom DNA Oligos from IDT; Coralville, Iowa).

In some embodiments of any of the aspects, the sequence variant beingdetected differentiates the African and American Zika virus strains. Insome embodiments of any of the aspects, the sequence variant is the SNPoccurring at site 7330 of the African (GenBank: KF268950) and American(GenBank: KU312312) Zika strains. In some embodiments of any of theaspects, the sgRNA has the sequence of SEQ ID NO: 1. In some embodimentsof any of the aspects, the method differentiates the African andAmerican Zika virus strains by detecting the presence or absence of theSNP occurring at site 7330 of the African (GenBank: KF268950) andAmerican (GenBank: KU312312) Zika strains, and the sgRNA has thesequence of SEQ ID NO:1.

Articles of Manufacture

In another aspect, the present invention provides articles ofmanufacture useful for detecting a virus or identifying a virus strain.In preferred embodiments, the article of manufacture is a kit fordetecting a virus, where the kit comprises a plurality of preservedpaper test articles and an electronic optical reader. Optionally, a kitcan further include instructions for performing the virus detectionand/or strain identification methods provided herein.

In some aspects of any of the embodiments, described herein is acomposition comprising a Cas nuclease and a sgRNA which can specificallybind to at least one sequence variant occurring in a population. In someaspects of any of the embodiments, described herein is a compositioncomprising a Cas9 nuclease and a sgRNA which can specifically bind to atleast one sequence variant occurring in a population, wherein thesequence variation occurs at the Cas9 PAM binding site.

In some aspects of any of the embodiments, described herein is acomposition comprising a Cas nuclease and a sgRNA which can specificallybind to at least one sequence variant occurring in a viral population.In some aspects of any of the embodiments, described herein is acomposition comprising a Cas9 nuclease and a sgRNA which canspecifically bind to at least one sequence variant occurring in a viralpopulation, wherein the sequence variation occurs at the Cas9 PAMbinding site.

In some aspects of any of the embodiments, described herein is acomposition comprising a Cas nuclease and a sgRNA which can specificallybind to at least one sequence variant occurring in a Zika viruspopulation. In some aspects of any of the embodiments, described hereinis a composition comprising a Cas9 nuclease and a sgRNA which canspecifically bind to at least one sequence variant occurring in a Zikavirus population, wherein the sequence variation occurs at the Cas9 PAMbinding site.

In some aspects of any of the embodiments, described herein is acomposition comprising a Cas nuclease and a sgRNA which can specificallybind to at least one sequence variant selected from Table 10. In someaspects of any of the embodiments, described herein is a compositioncomprising a Cas9 nuclease and a sgRNA which can specifically bind to atleast one sequence variant selected from Table 5, wherein the sequencevariation occurs at the Cas9 PAM binding site.

In some aspects of any of the embodiments, described herein is acomposition comprising a Cas9 nuclease and a sgRNA comprising SEQ IDNO:1. In some aspects of any of the embodiments, described herein is acomposition comprising a Cas9 nuclease and a sgRNA comprising SEQ IDNO:1, wherein the sequence variation occurs at the Cas9 PAM bindingsite. In some embodiments of any of the aspects, the sgRNA consists ofSEQ ID NO:1.

In some aspects of any of the embodiments, described herein is a sgRNAwhich can specifically bind to a sequence flanking at least one sequencevariant selected from Table 5, wherein the sequence variation occurs ata Cas9 PAM binding site. In some aspects of any of the embodiments,described herein is a composition a sgRNA comprising SEQ ID NO:1. Insome aspects of any of the embodiments, described herein is acomposition a sgRNA consisting of SEQ ID NO:1.

Methods for sgRNA selection and design are described elsewhere herein.In some embodiments of any of the aspects, a sgRNA which canspecifically bind to a sequence flanking a given sequence variant cancomprise a 20 nt sequence complementary to a sequence found from 1-30nucleotides from the sequence variation. In some embodiments of any ofthe aspects, a sgRNA which can specifically bind to a sequence flankinga given sequence variant can comprise a 20 nt sequence complementary toa sequence found from 1-25 nucleotides from the sequence variation. Insome embodiments of any of the aspects, a sgRNA which can specificallybind to a sequence flanking a given sequence variant can comprise a 20nt sequence complementary to a sequence found from 1-20 nucleotides fromthe sequence variation.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which the invention pertains. All definitions, as defined andused herein, should be understood to control over dictionarydefinitions, definitions in documents incorporated by reference, and/orordinary meanings of the defined terms.

All references, patents and patent applications disclosed herein areincorporated by reference with respect to the subject matter for whicheach is cited, which in some cases may encompass the entirety of thedocument.

The indefinite articles “a” and “an,” as used herein in thespecification and in the claims, unless clearly indicated to thecontrary, should be understood to mean “at least one.”

The phrase “and/or,” as used herein in the specification and in theclaims, should be understood to mean “either or both” of the elements soconjoined, i.e., elements that are conjunctively present in some casesand disjunctively present in other cases. Multiple elements listed with“and/or” should be construed in the same fashion, i.e., “one or more” ofthe elements so conjoined. Other elements may optionally be presentother than the elements specifically identified by the “and/or” clause,whether related or unrelated to those elements specifically identified.Thus, as a non-limiting example, a reference to “A and/or B”, when usedin conjunction with open-ended language such as “comprising” can refer,in one embodiment, to A only (optionally including elements other thanB); in another embodiment, to B only (optionally including elementsother than A); in yet another embodiment, to both A and B (optionallyincluding other elements); etc.

As used herein in the specification and in the claims, “or” should beunderstood to have the same meaning as “and/or” as defined above. Forexample, when separating items in a list, “or” or “and/or” shall beinterpreted as being inclusive, i.e., the inclusion of at least one, butalso including more than one, of a number or list of elements, and,optionally, additional unlisted items. Only terms clearly indicated tothe contrary, such as “only one of” or “exactly one of,” or, when usedin the claims, “consisting of,” will refer to the inclusion of exactlyone element of a number or list of elements. In general, the term “or”as used herein shall only be interpreted as indicating exclusivealternatives (i.e. “one or the other but not both”) when preceded byterms of exclusivity, such as “either,” “one of,” “only one of,” or“exactly one of” “Consisting essentially of,” when used in the claims,shall have its ordinary meaning as used in the field of patent law.

As used herein, “about” means within 5% of a stated concentration rangeor within 5% of a stated time frame.

It should also be understood that, unless clearly indicated to thecontrary, in any methods claimed herein that include more than one stepor act, the order of the steps or acts of the method is not necessarilylimited to the order in which the steps or acts of the method arerecited.

Having now described the invention, the same will be illustrated withreference to certain examples, which are included herein forillustration purposes only, and which are not intended to be limiting ofthe invention.

EXAMPLES

Reference is now made to the following examples, which together with theabove descriptions illustrate the invention in a non-limiting fashion.

Example 1: Rapid, Low-Cost Detection of Zika Virus Using ProgrammableBiomolecular Components

Materials and Methods

In Silico Sensor Design and DNA Synthesis:

A set of 48 toehold switch sensors and corresponding NASBA primers weregenerated using an integrated in silico design algorithm.

DNA Sensor Assembly:

Toehold switch constructs were amplified from DNA templates (IntegratedDNA Technologies) and ligated to the lacZ reporter gene via PCR.Plasmids were constructed for characterization of the top six toeholdswitches (FIG. 3A). The DNA templates were amplified using PCR andinserted into pET system parent plasmids (EMD Millipore) using Gibsonassembly (Gibson et al., 2009) with 30 bp overlap regions. Plasmids forsensors 27B and 32B are available through Addgene (plasmid numbers:75006-75011).

Cell-Free Reactions:

Details of RNA sensor validation are described in Pardee et al. (2014).Briefly, amplified sensor DNA was column purified and tested on paperdiscs (2 mm) containing freeze-dried, cell-free reactions (NEB,PURExpress) in the presence or absence of trigger RNA coding for acomplementary region of the Zika virus genome (128-178 nts). Thecell-free reactions consisted of: NEB Solution A (40%) and B (30%),chlorophenol red-b-D-galactopyranoside (Sigma, 0.6 mg/ml), RNaseinhibitor (Roche, 03335402001; 0.5%), and linear DNA constructs encodingthe toehold sensors (0.33 nM). The paper discs (Whatman, 1442-042) wereblocked in 5% BSA overnight prior to use. Trigger RNA was produced usingT7 RNAP-based transcription (Epicenter ASF3257) from linear DNAtemplates. Paper-based reactions (1.8 μl) were incubated at 37° C. usingeither our companion electronic reader inside a humidified chamber or aplate reader (BioTek Neo). For the in-house reader, paper discs wereplaced into 2 mm holes in a removable acrylic chip; for the platereader, paper discs were placed into black, clear bottom 384-well plates(Corning 3544).

NASBA:

For NASBA reactions, the trigger elements (128-178 nts) were extended by100 nts on the 5′ and 3′ ends with the relevant Zika genome sequence toprovide suitable template RNAs. RNA amplicons were spiked into 7% humanserum (Sigma H4522) where indicated. Reaction Buffer (Life SciencesNECB-24; 33.5%), Nucleotide Mix (Life Sciences NECN-24; 16.5%), RNaseinhibitor (Roche, 03335402001; 0.5%), 12.5 mM of each NASBA primer (2%),nuclease free water (2.5%), and RNA amplicon (20%) were assembled at 4°C. and incubated at 65° C. for 2 min, followed by a 10 min incubation at41° C. Enzyme Mix (Life Sciences NEC-1-24; 25%) was then added to thereaction (for a final volume of 5 and the mixture was incubated at 41°C. for 2 hr. unless noted otherwise. For output reads with paper-basedtoeholds, the NASBA reactions were diluted 1:7 in water. See Table 2 forprimer sequences.

Lentivirus Preparation and Processing:

HEK293FT cells (Life Technologies, R70007) used for virus packaging werecultured in DMEM supplemented with 10% FBS, 1% penicillin-streptomycin,and 4 mM GlutaMAX (ThermoFisher Scientific). 12 hr. prior totransfection, 6.5×10⁶ cells were seeded in a 10 cm dish. 7.5 mg psPAX2,2.5 mg pMD2.G, and 10 mg pSB700 modified to include a Zika or Dengue RNAfragment were transfected using the HeBS—CaCl₂ method. Media was changed12 hr. post-transfection. 27 hr. after changing media, viral supernatantwas harvested and filtered using a 0.45 mm syringe filter. Viralsupernatant was then purified with ViraBind Lentivirus Purification Kit(Cell Biolabs VPK-104) and buffer exchanged into 1×PBS with Lenti-XConcentrator (Clontech, 631231). Viral RNA concentration was quantifiedusing QuickTiter Lentivirus Quantification Kit (VPK-112). Virus sampleswere spiked into 7% human serum at a final volume of 25 μl. Samples wereheated to 95° C. for 1 and 2 min and used as input to NASBA.

Zika Virus Preparation and Processing:

100 μl of Zika virus isolate (MR 766) was utilized for infection of 106Vero cells in 4 ml of media (DMEM supplemented with 2% fetal calf serum[FCS] and penicillin-streptomycin). The supernatant was removed after 2hr. of incubation at 37° C. and replaced with fresh media (DMEM, 10%FCS) for 48 hr. of infection. Cell debris was removed by centrifugationat 1,500 rcf for 10 min, and aliquots of the virus were stored at −80°C. until use. The virus was buffer exchanged into 1×PBS with Lenti-XConcentrator (Clontech, 631231). Viral RNA concentrations weredetermined from virus purified with the QIAamp Viral RNA Mini Kit(QIAGEN 52904) and confirmed with qRT-PCR. The titer of the Zika virusused was 6.7×10⁷ infectious units per milliliter (Lambeth et al., 2005).Virus samples were spiked into 7% human serum at a final volume of 30μl. Samples were heated to 95° C. for 2 min and used as input to NASBA.NASBA primers were re-designed to accommodate the MR 766 strainsequence.

Dengue Orthogonality:

Genomic RNA from three Dengue serotypes was purified using the QIAampViral RNA Mini Kit (QIAGEN 52904). Dengue 1 (GenBank: KM204119), Dengue2 (GenBank: KM204118), Dengue 4 (GenBank: AF326573). NASBA reactionsusing the sensor 32B primer set were performed on 30 pM RNA for 2 hr.NASBA reactions were diluted 1:7 in water and used to rehydratefreeze-dried, paper-based reactions containing sensor 32B.

Electric Optical Reader:

The portable device consists of four layers housed within a laser-cutacrylic box fastened together with metal screws and mounting brackets(FIG. 7; McMaster-Carr, 8505K14, 98164A061; Digi-Key, 36-621-ND). Thetop layer holds a multiplexer (Sparkfun, BOB-09056), solderablebreadboard (Sparkfun, PRT-12702), friction lock connectors (Digi-Key,A31001-ND, A19473-ND) and 16 LEDs (Digi-Key, 754-1262-ND). The LEDs havea very narrow viewing angle and an emission of 570 nm to match theabsorbance maximum of the chlorophenol red product from the LacZreaction. The LEDs were placed in close proximity to the chip in themiddle layer, which holds 16 paper disks within 2 mm apertures. Theapertures prevented transmission of stray light and were coaxial withthe LEDs in the top layer and the array of 16 TSL2591 sensors (Adafruit,1980) in the third layer below, which also contained two solderablebreadboards and connectors as above. The bottom layer contains theArduino Uno with an attached Power Shield (Adafruit, 2708) connected toa rechargeable 2,000 mAh lithium ion battery (Adafruit, 2011) on which adatalogging shield (Adafruit, 1141) was stacked with connectors(Digi-Key, A30954-ND, A19476) and a 4 GB SD/MicroSD Card (Adafruit,102). To prevent crosstalk between reads, reactions were read in seriesby sequentially activating each LED and sensor pair. The read frequencyand pattern of the reader can be easily adjusted by modifying anduploading alternative sketches to the Arduino. The raw data (which isthe median of 29 100 ms, 4283 gain reads per minute) was saved to the SDcard along with the date and time of the run, integration time and gainsettings. The data were processed with the MATLAB script and graphed inPrism. A diagram of the circuit and an overview of the laser cut partscan be found in FIG. 7, and laser cutting patterns, the Arduino sketch,and MATLAB script are in Appendix A.

Calculation of Fold Change:

The calculation of fold change for plate reader data was done by firstsubtracting the background absorbance measured from paper-basedreactions that did not contain sensor DNA or trigger RNA. Thesenormalized values were smoothed to reduce measurement noise using athree-point average of the time point and the data collected 10 minbefore and after. The minimum value of each well was then adjusted tozero. For data presented in FIGS. 3, 6, and 10, fold change wascalculated from these zero adjusted values by dividing the wells at eachtime point by the average signal from the corresponding sensor-alonecontrol wells. For our initial sensor screen (FIG. 2), we used a moresensitive measure of fold change based on the difference in the rate ofcolor change between control and RNA trigger wells. This was done bycalculating the rate of change in normalized absorbance (570 nm) valuesusing slope; where, at each 10 min time point, the rate was calculatedusing Sn=(T_(n+1)−T_(n))/10, where T is the normalized data at a timepoint (T_(n)) and the time point 10 min later (T_(n+1)), and S_(n) isthe slope reported for T_(n). Fold change was then calculated as above.MATLAB script to analyze data collected on a plate reader is provided inAppendix A.

NASBA-CRISPR Cleavage (NASBACC):

Reactions were performed in a 5 μl volume containing (NASBA buffer), 1μl of a 250 nM Cas9 nuclease (NEB, M0386), and 250 nM purified gRNA(GeneArt precision gRNA synthesis kit, ThermoFisher Scientific, A29377)mix, 3 nM NASBACC primers, and 0.4 units of RNase inhibitor (NEB,M0314). The forward NASBACC primer is composed of the reverse complementof the trigger H sequence (5′-GTT TGA ATG AAT TGT AGG CTT GTT ATA GTTATG TTT-3′ (SEQ ID NO: 3)) and the forward binding sequence of the(region 32) NASBA primers. The reverse NASBACC primer contains the T7promoter sequence (5′-CTA ATA CGA CTC ACT ATA GG-3′ (SEQ ID NO: 4))followed by the reverse binding sequence of the (region 32) NASBAprimers. The assembled reaction was incubated at 37° C. for 2 to 6hours. For toehold activation assay on freeze-dried paper, NASBACCreactions were diluted 1:10 in nuclease-free water.

Zika Virus Stock Production for Macaque Infection:

ZIKV strain H/PF/2013 (GenBank accession number: KJ776791), originallyisolated from a 51-year-old female in France returning from FrenchPolynesia with a single round of amplification on Vero cells, wasobtained from Xavier de Lamballerie (European Virus Archive, MarseilleFrance). Virus stocks were prepared by inoculation onto a confluentmonolayer of C6/36 mosquito cells. A single harvest of virus with atiter of 1.26×10⁶ PFU/ml for the Asian-lineage (equivalent to 1.43×10⁹vRNA copies/ml) was used.

Viremic Plasma Processing:

All Indian-origin rhesus macaque monkeys from which plasma was isolatedwere cared for by the staff at the Wisconsin National Primate ResearchCenter (WNPRC) in accordance with the regulations and guidelinesoutlined in the Animal Welfare Act and the Guide for the Care and Use ofLaboratory Animals and the recommendations of the Weatherall report.This study was approved by the University of Wisconsin-Madison GraduateSchool Institutional Animal Care and Use Committee (Animal Care and UseProtocol Number G005401). For all procedures (i.e., physicalexamination, virus inoculation, blood and swab collection), animals wereanesthetized with an intramuscular dose of ketamine (10 ml/kg). Bloodsamples were obtained using a vacutainer system or needle and syringefrom the femoral or saphenous vein. For processing, plasma was diluted1:10 in nuclease free water, heated to 95° C. for 2 min, and immediatelyadded to a NASBA reaction. NASBA was run for 3 hr.

Zika Virus Challenge of Macaques, Plasma Collection, and Processing:

The virus stock was thawed, diluted in PBS to the appropriateconcentration for each challenge, and loaded into a 1 ml syringe thatwas kept on ice until challenge. Animals were anesthetized as describedabove, and 1 ml of inocula was administered subcutaneously over thecranial dorsum. At the conclusion of the procedure, animals were closelymonitored by veterinary and animal care staff for adverse reactions andsigns of disease. Fresh plasma and PBMC were isolated from EDTA-treatedwhole blood by Ficoll density centrifugation at 1860 rcf for 30 min. Theplasma layer was collected and centrifuged for an additional 8 min at670 rcf to remove residual cells. The supernatant plasma was thenfiltered over a 0.45 μm syringe filter. Collected plasma was diluted1:10 in nuclease free water. Diluted samples were heated to 95° C. fortwo minutes and immediately added to a NASBA reaction as describedabove. NASBA was run for three hours.

qRT-PCR to Determine Macaque Plasma Viral Loads:

Viral RNA was extracted from 300 μl of plasma using the Viral TotalNucleic Acid Purification Kit (Promega) on a Maxwell 16 MDx instrument.Viral RNA was quantified by qRT-PCR using the primers and probe designedby Lanciotti et al. (2008). The RT-PCR was performed using theSuperScript III Platinum one-step quantitative RT-PCR system(Invitrogen) on the LightCycler 480 instrument (Roche Diagnostics).Primers and probe were used at final concentrations of 600 nm and 100nm, respectively, along with 150 ng random primers (Promega). Cyclingconditions were as follows: 37° C. for 15 min, 50° C. for 30 min, and95° C. for 2 min, followed by 50 cycles of 95° C. for 15 seconds and 60°C. for 1 min. Virus concentration was determined by interpolation ontoan internal standard curve composed of seven 10-fold serial dilutions ofa synthetic ZIKV RNA fragment based on the Asian lineage.

Results

In Silico Toehold Switch Design:

Toehold switch sensors are programmable synthetic riboregulators thatcontrol the translation of a gene via the binding of a trans-actingtrigger RNA. The switches contain a hairpin structure that blocks genetranslation in cis by sequestration of the ribosome binding site (RBS)and start codon. Upon a switch binding to a complementary trigger RNA,sequestration of the RBS and start codon is relieved, activating genetranslation (FIGS. 2A-2B) (Green et al., 2014). To allow forcolorimetric detection of trigger RNA sequences, the sensors can bedesigned to regulate translation of the enzyme LacZ, which mediates acolor change by converting a yellow substrate (chlorophenolred-b-D-galactopyranoside) to a purple product (chlorophenol red).

Toehold switch sensors for sequence-based detection of Zika virus weregenerated using an expanded version of the previously developed insilico design algorithm (Green et al., 2014). The modified algorithmscreened the genome of the Zika strain prevalent in the Americas(Genbank:KU312312) for regions compatible with RNA amplification andtoehold switch activation. The selected Zika genome regions were thencomputationally filtered to eliminate potential homology to the humantranscriptome and to a panel of related viruses, including Dengue andChikungunya. A total of 24 unique regions of the Zika genome compatiblewith downstream sensing efforts were identified.

Two toehold switches, each utilizing a different design scheme, weredesigned for each region, resulting in a total of 48 sensors. The firstdesign scheme, termed the A series, utilizes a modification to theoriginal toehold switch (Green et al., 2014) that reduces the size ofthe loop domain from 18 nts to 11 nts (FIG. 2A) to discourageloop-mediated docking of the ribosome and therefore reduce leakage inthe OFF state. The second design scheme, termed the B series, features a12-nt loop and incorporates a more thermodynamically stable stem inorder to lower OFF state gene expression (FIG. 2B).

Rapid In Vitro Sensor Assembly and Screening:

In vitro assembly and initial screening of all 48 sensors took place ina 7 hr. time period, with low costs associated with sensor development(DNA input $20 USD/sensor) and testing ($0.10-$1/test). All 48 sensorsand 24 targeted genomic regions were assembled in-house using in vitroprotocols. Toehold switches were constructed by ligating the sensors(˜130 nt) to a LacZ reporter element in a single 2 hr. PCR-based step.Sensor performance screening to assess each sensor against itsrespective trigger RNA element (Zika genome fragment) was completedusing low volume, cell-free transcription and translation reactions onpaper. We found that 25 (52%) of the 48 sensors produce a fold change offive or greater in the presence of the appropriate trigger element(128-178 nucleotide regions of the Zika genome; FIGS. 2C, 2D). Thetop-ranked sensors exhibited activation as high as 34-fold over sensoralone (sensor 27B) and were activated in as quickly as 20 minutes afterincubation at 37° C. (sensors 7A and 8A). For all sensors, maximum foldchange occurred within the first 90 min. Averaging the LacZ output fromsensors not exposed to trigger RNA confirmed that the low backgrounddesign of the series B toehold switch sensors successfully reducedsignal leakage (FIG. 2D, inset).

Assessing and Improving Zika Virus Sensor Sensitivity:

We selected top performing sensors from both the A and B series fortrigger RNA titration experiments and found that all chosen sensors wereactivated with as little as 30 nM of trigger RNA (FIG. 3A). The sensorsdisplayed a linear response to RNA concentration, providingsemi-quantitative information on input trigger RNA values (FIG. 4A).Additionally, our top three sensors were highly orthogonal to each otherwhen challenged with a high dose of trigger RNA from off-target Zikasequences (3,000 nM) (FIG. 4B).

Though the sensors displayed specificity for their respective Zika RNAtrigger, they were unable to detect clinically relevant RNAconcentrations. Zika viral loads have been documented as high as 202×10⁶copies/ml (365 fM) in urine (Gourinat et al., 2015). However, viralloads in saliva and serum are reportedly even lower, with 3×10⁶copies/ml (4.9 fM) (Barzon et al., 2016) documented in patient salivaand 2.5×10⁶ copies/ml (4.1 fM) (Zika Experimental Science Team, 2016)and 7.2×10⁵ copies/ml (1.2 fM) (Lanciotti et al., 2008) in primate andpatient serum, respectively. Accordingly, to increase the sensitivity ofour diagnostic platform, we incorporated an isothermal RNA amplificationtechnique known as NASBA (nucleic acid sequence-based amplification)into our workflow (FIG. 1).

NASBA is a promising candidate for use with our diagnostic schemebecause it is known to be extremely sensitive and has a proven trackrecord in field-based diagnostic applications (Cordray andRichards-Kortum, 2012). The amplification process begins with reversetranscription of a target RNA that is mediated by a sequence-specificreverse primer to create an RNA/DNA duplex. RNase H then degrades theRNA template, allowing a forward primer containing the T7 promoter tobind and initiate elongation of the complementary strand, generating adouble-stranded DNA product. T7-mediated transcription of the DNAtemplate then creates copies of the target RNA sequence. Importantly,each new target RNA can be detected by the toehold switch sensors andalso serve as starting material for further amplification cycles. NASBArequires an initial heating step (65° C.), followed by isothermalamplification at 41° C. (FIG. 3B) (Guatelli et al., 1990).

NASBA was performed on trigger RNA corresponding to Zika genomic regionsfor sensors 27B and 32B. Trigger RNAs were spiked into either water orhuman serum (7%) to more closely mimic clinical samples. NASBA reactionswere run for 2 hr. and then applied to freeze-dried, paper-basedsensors. We saw detection with Zika sensors from NASBA reactionsinitiated with as little as 3 fM of trigger RNA (FIG. 3C), a valuewithin the range of reported patient viral loads. Zika sensor detectionof NASBA-amplified trigger RNA proved to be reliable on samples spikedinto either serum or water (FIG. 4C). Additionally, for reactionsinitialized with high concentrations of trigger RNA (>300 fM), NASBAreaction times could be reduced to as little as 30 minutes (FIG. 4D).NASBA reagents are compatible with freeze-drying (FIG. 4E) and couldtherefore be easily deployed and utilized alongside our paper-basedsensors. We also demonstrated that NASBA can be run in the absence ofthe initial heating step (65° C.) (FIG. 4F), further reducing thetechnical and power requirements for deployment.

Field-Ready Diagnostic Platform:

To move our experiments toward conditions more representative of thosefound in clinics worldwide, we focused on three key efforts: (1) testingsensor specificity against related viruses that share clinical symptoms,partial homology, and geographic range with Zika virus; (2) building asecond-generation portable, battery-powered reader to providelab-quality results in low resource environments; and (3) developing alow-cost and tractable method for viral RNA extraction.

Although our sensor design algorithm screened for Zika genomic sequencesthat are mostly distinct from those of related viruses, the targetedZika sequences do share substantial similarity (51%-59%) with theirDengue virus counterparts (FIGS. 5A-5B). To test the Zika sensors forpossible cross-reactivity, we exposed the sensors to regions of theDengue genome that share a degree of homology with regions targeted inthe Zika genome. Sensors 27B and 32B were treated with highconcentrations of RNA amplicons (3,000 nM) from either Zika or Denguegenomic regions. As seen in FIG. 6A, Dengue RNA sequences failed toactivate the toehold switch sensors. We also tested our NASBA primersets for specificity to their targeted Zika sequences by applying theNASBA-mediated amplification and paper-based detection scheme to 300 fMinputs of the Dengue and Zika RNA in human serum (7%). Again, noresponse to the Dengue RNA sequences was observed, demonstrating robustsequence specificity in our amplification and detection scheme (FIG.6B).

As part of our efforts to advance the paper-based sensor platform towardfield-ready diagnostics, we designed a second generation portableelectronic reader to serve as an accessible, low-cost companiontechnology that provides robust and quantitative measurements of sensoroutputs. The electronic reader was assembled using readily availableconsumer components, open-source code, and laser-cut acrylic housing,with a total cost of just under $250 (FIG. 7 and Table 3). The reader ispowered by a lithium ion battery (18.5 hr.) that can be re-charged viamicro USB and houses onboard data storage (4 GB) to resolve the need foran attached laptop during diagnostic reads (Pardee et al., 2014). Toachieve sensitive detection of toehold switch signal output, an acrylicchip that holds the freeze-dried, paper-based reactions is placed intothe reader between an LED light source (570 nm) and electronic sensors(FIG. 7B). Using onboard electronics, each sample is read 29 times perminute, providing low-noise measurements of changes in lighttransmission due to LacZ-mediated color change.

To demonstrate the utility of the companion reader, we monitoreddetection of 1 fM and 3 fM of Zika RNA amplicons that had been amplifiedin NASBA reactions for 2.5 hr. The reader detected significant signalfrom both samples, which are within the reported range of Zika virus inpatient serum (1.2 fM) and urine (365 fM) (Gourinat et al., 2015;Lanciotti et al., 2008), after just over 20 min (FIG. 6C).

Our next challenge was to develop a technique to release RNA from theviral capsid using simple methodology compatible with low-resourceenvironments. To this end, we tested the efficacy of boiling viralsamples to break down the capsid. For initial development, we engineeredlentivirus, which is also an RNA virus, to encapsulate the regions ofeither the Zika or Dengue genomes that correspond to the sensor 32Btarget sequence (FIG. 5B). These proxy Zika and Dengue viruses werespiked into human serum (7%) at a final concentration of 3 fM and heatedto 95° C. for either 1 or 2 min. The resulting lysates were thenimmediately used to initiate NASBA reactions, in order to simulate whatmight be recovered from a patient sample. Boiling the viral samples forone minute was sufficient to release detectable amounts of RNA in ouramplification and toehold switch detection scheme (FIG. 5C). NASBAreactions from 2 min boiled samples were also monitored for sensoractivation on the portable electronic reader. We detected strong sensoractivation in less than 30 minutes from 3 fM of lentivirus carrying ZikaRNA. We were also able to demonstrate clear discrimination betweenlentiviruses containing Zika and Dengue RNA sequences (FIG. 6D).

NASBA-CRISPR Cleavage Assay to Discriminate Between Zika Strains:

During epidemic outbreaks, it is often valuable to monitor pathogenlineage and geographic spread. In some cases, genetic variants may beresponsible for different clinical manifestations of infection. Forexample, the Zika strain found in Brazil has been uniquely connectedwith higher incidences of fetal microcephaly and Guillain-Barré syndrome(Calvet et al., 2016; Mlakar et al., 2016). To allow for strain-specificdetection and tracking, we developed an assay that provides single-basediscrimination in a manner that is compatible with our freeze-driedsensor platform. Our assay, which we term NASBA-CRISPR Cleavage(NASBACC), leverages the sequence-specific nuclease activity ofCRISPR/Cas9 to discriminate between viral lineages (FIG. 8A). To dothis, NASBACC exploits the ability of Cas9 to selectively cleave DNAonly in the presence of an NGG protospacer adjacent motif (PAM). Sinceany non-biased mutation has a 48% probability of either creating a newPAM site or destroying an existing one (Table 4), there are manystrain-specific PAM sites that can be used for lineage discrimination(FIGS. 8B-8C). In the NASBACC detection scheme, RNA sequences undergoNASBA amplification utilizing a reverse primer designed to append thetrigger sequence of a synthetic toehold switch (sensor H, FIG. 8A)(Pardee et al., 2014). In the presence of the appropriate PAM sequenceand guide RNA target site, the double-stranded DNA that is synthesizedas part of the NASBA reaction undergoes Cas9-mediated cleavage,resulting in a truncated RNA product that is unable to activate thesensor H toehold switch. In the absence of the PAM sequence, thefull-length RNA product containing the sensor H trigger sequence isgenerated, allowing for sensor H activation. Trigger RNA is onlyamplified from DNA that is not cut by Cas9, thereby allowing forstrain-specific detection using toehold sensor H.

Using the paper-based system, sensor 32B was able to distinguish betweenZika and Dengue RNA sequences. However, this sensor could notdiscriminate between the African (GenBank: KF268950) and American(GenBank: KU312312) Zika variants (FIG. 8D), a feature that may beuseful in certain diagnostic applications. To address this, we appliedour NASBACC detection scheme to discriminate between the African andAmerican Zika strains. Due to a single-base difference in the triggerregions of these two strains, a PAM site only exists in theAmerican-lineage sequence (FIG. 8C). Thus, only the American strainsequence was cleaved by Cas9, which led to amplification of truncatedRNA that did not activate the sensor H toehold switch (FIG. 8E).Conversely, the African strain sequence does not contain the PAM siteand was not cleaved by Cas9, which resulted in amplification offull-length RNA that activated the sensor H toehold switch.Incorporating NASBACC into our diagnostic workflow can provide precisegenotypic information within a few hours. As with the other biomolecularelements of this workflow, Cas9 is compatible with lyophilization andcould be used in the field (FIG. 9).

Diagnostic Workflow Validation with Active Zika Virus:

We next sought to validate our sensor platform with live Zika virus.First, we verified that our amplification and detection scheme couldsuccessfully detect full-length genomic RNA purified from Zika virus(Uganda strain MR 766) (FIG. 10A). We designed new NASBA primers toaccommodate sequence differences between the Uganda Zika strain(GenBank: AY632535) and the American Zika strain (GenBank: KU312312)that our sensors and primers had originally been designed to detect.Computational analysis suggested that Uganda-lineage Zika RNA wouldactivate sensor 32B despite two base mismatches in the toehold region,and this was confirmed experimentally (FIG. 10A). We also demonstratedsensor orthogonality to full length genomic Dengue RNA isolated fromthree different Dengue serotypes using these methods (FIG. 10A).

Once we confirmed that the sensors behaved as expected on full-lengthgenomic RNA, we sought to validate the sample preparation scheme anddiagnostic workflow from start to finish. Active Zika virus was culturedin the laboratory and spiked into human serum (7%) at a finalconcentration of 10 fM, to mimic a clinical sample. The viral sample wasthen heated to 95° C. for 2 min, and the resulting lysate was subjectedto NASBA amplification for three hours. Sensor activation from theNASBA-amplified viral sample was monitored on the portable electronicreader. We successfully detected activation of sensor 32B from adiagnostic workflow initiated with live Zika virus (FIG. 10B).

For the final validation of our system, we acquired and tested plasmasamples from a viremic macaque infected with Zika virus (GenBank:KJ776791) (Zika Experimental Science Team, 2016). The macaque was foundto have a plasma viral load of 1.7×10⁶ copies/ml (2.8 fM) by a standardqRT-PCR protocol, which was within the detection limits of our platformas tested on synthetic RNA amplicons (FIG. 6C). The viremic plasma wasdiluted 1:10 in water to reduce known inhibitory effects of plasma ondownstream reactions and was then taken through our sample processingand diagnostic workflow. The sample was heated to 95° C. for 2 min andthen amplified via NASBA for 3 hr. Paper-based reactions were monitoredon the portable electronic reader and showed strong activation with bothsensors 27B and 32B in less than 30 min (FIGS. 10C-10D).

In Silico Strategy for Toehold Switch Sensor and NASBA Primer Design.

An integrated in silico strategy was developed for generating optimalNASBA primers and toehold switches for detection of Zika. Mirroring theprocedure used for running the paper-based diagnostic assay, a set ofoptimal primers was initially generated for the NASBA reaction and thena series of toehold switch designs screened for activity on the RNAtranscripts produced by NASBA was developed.

Identification of Optimal NASBA Primers for Zika Amplification.

A set of potential primer pairs with favorable characteristics for NASBAreactions as described by Deiman et al. (Deiman et al., 2002) wasgenerated. The Zika genome was analyzed to identify all potentialforward and reverse priming sites that had the followingcharacteristics:

-   -   GC content between 40-60%    -   Template hybridization regions of 20- to 24-nts and with DNA        melting temperatures above 41° C.    -   No consecutive runs of four or more nucleotides    -   An A base at the final 3′ nucleotide    -   Minimal DNA primer internal secondary structure, including the        T7 promoter region    -   Minimal DNA primer dimer formation probability    -   Higher GC content in the 6-nts at the 5′ end of the primer that        hybridized to the template    -   Higher AT content in the 6-nts at the 3′ end of the primer

All subsequences from the Zika genome that did not satisfy requirements1 to 4 were immediately eliminated from consideration. The remainingprimers were then analyzed for characteristics 5-8 and the deviationfrom optimal 50% GC content, with each parameter converted into anumerical score. The forward NASBA primers, which append the T7 promotersite to NASBA DNA intermediate, were modeled with this T7 promoter sitepresent. Accordingly, the prefix sequenceAATTCTAATACGACTCACTATAGGGAGAAGG (SEQ ID NO: 5) (T7 promoter sequenceunderlined) was appended to the 5′ end of each forward primer. Theresulting scores were combined and used to estimate the overallfavorability of every potential primer in the Zika genome. Followingthis initial screen, the top 2% of all the potential primers were thencompared to the rest of the Zika genome to determine the longestcontiguous region of the primer that matched more than one site in thegenome. This comparison provided a coarse check of primer specificity inadvance of more detailed primer specificity screening conducted later inthe design process. The length of this contiguous region for each primerwas then incorporated into a final score for each primer.

The first stage of screening resulted in a set of forward and reverseprimers to provide optimal characteristics for binding to the targetgenome; however, it did not consider other important effects on NASBAefficiency, namely the length and secondary structure of the ampliconproduced by NASBA. To consider these amplicon-related effects, thebinding sites for each primer on the genome were identified and, if morethan one primer acted at the same site, the primer awarded the highestfavorability score was selected. A set of potential forward and reverseprimer pairs was constructed based on the recommended amplicon lengthsfor successful NASBA reactions. Although NASBA is known to work bestwith amplicons having lengths between approximately 120-nts to 250-nts(Deiman et al., 2002), this rapid screening approach initially employssynthetic DNA strands as templates for transcribing the target RNA.Since the length of these DNA oligos (IDT Ultramers) is currentlylimited to 200-nts including the T7 promoter site, primer pairs wereinstead examined for amplicons ranging from 120- to 176-nts in length.After applying all the above constraints on primer and ampliconsequences, a set of 4351 potential NASBA primer pairs remained. The RNAamplicons generated for each of these primers pairs were then assessedfor their secondary structure. NASBA reactions are known to be moreeffective when applied to templates having low secondary structure.Consequently, the degree of amplicon single-strandedness was examinedusing the NUPACK ensemble defect function (Zadeh et al., 2011a, 2011b).

Next, each of the potential NASBA primers were then coarsely screenedfor sequence similarities with 11 viruses known to be closely related toZika: Dengue virus 1, Dengue virus 2, Dengue virus 3, Dengue virus 4,West Nile virus, St. Louis encephalitis virus, yellow fever virus,Powassan virus, Semliki Forest virus, O'nyong'nyong virus, andChikungunya virus. Sequence similarities were estimated by determiningthe maximum contiguous sequence in the primer that was found in any ofthe 11 related viruses. More stringent specificity screening was carriedout in later stages as described below.

After all the above screening procedures, the final NASBA primer pairswere sorted by quality after taking into account the favorability scoresof each primer, the secondary structure of the amplicon, and thepotential for non-specific binding with other viruses.

Identification of Optimal Toehold Switches for NASBA Products.

Out of the 4351 NASBA amplicons, the top 1025 were selected as potentialtargets for toehold switches. The in silico design process for thesetoehold switches followed closely that previously used for designingmRNA sensors in vivo (Green et al., 2014) and on paper (Pardee et al.,2014). Briefly, toehold switch mRNA sensors were designed thathybridized to the NASBA amplicon at 1-nt increments. This sliding windowencompassed the internal region of the NASBA product outside of theprimer binding sites. This internal region was selected to avoid anypotential for sensor activation or competitive binding by residual NASBAprimers. The resulting toehold switches were analyzed for secondarystructure and toehold availability, and screened to eliminate anysensors with unwanted in-frame stop codons in the output gene sequence.The target transcript itself was again assayed for single-strandednessand availability of the sensor binding sites. The above factors wereincorporated into a sensor design score as described previously (Greenet al., 2014). The highest scoring toehold switch sensor for eachamplicon was then passed on to the final selection stage.

Final Design Selection Process.

After the above screening and design stages, the set of 1025 NASBAprimer pairs was assembled with corresponding optimized toehold switchsensors. The top overall designs were selected by combining thefavorability scores obtained from the NASBA and toehold switchevaluation steps. The primer and sensor sequences from these top designswere then tested for specificity against the human transcriptome and thesame panel of closely related viral genomes listed above usingNCBI/Primer-BLAST. Moreover, they were screened for specificity withinthe Zika genome itself. Ultimately, the top 24 designs that survived thePrimer-BLAST specificity stage were selected for testing using our rapidin vitro screening approach.

Modifying the Toehold Switch Sensor Design for Decreased Signal Leakage.

Detailed studies of the toehold switch design parameters (Green et al.,2014) and thermodynamic considerations suggested two simple strategiesfor decreasing leakage from the toehold switches: reducing the size ofthe loop containing the ribosome binding site (RBS) in the sensor, andfurther stabilization of the sensor stem. Both these strategies wereapplied in the Zika-specific toehold switches.

The ON and OFF state signals from the toehold switches increase as thesize of the loop in the switch RNA increases. This effect is likely dueto two factors: increased accessibility of the RBS to the ribosome,which promotes translation in the presence or absence of the target RNA;and entropic effects that discourage stem formation as the loop becomeslonger. Conversely, decreasing the size of the loop is associated withlower leakage, albeit with a decrease in ON state activity. Stabilizingthe switch RNA stem by adding additional base pairs or by eliminatingthe downstream refolding domain (Green et al., 2014) increases the freeenergy required to unwind the sensor stem and thus encourages decreasedsignal leakage.

In accordance with above factors, two different types of toeholdswitches were tested aiming to lower leakage. The first type of sensor,referred to as the A series, are nearly identical to those previouslyused for mRNA sensing (Green et al., 2014; Pardee et al., 2014), excepttheir loop domain has been reduced from 18-nts to 11-nts. These Asensors retained the downstream refolding domain to encourage sensortriggering and they all have the same sequence at the top of the sensorstem-loop (GUUAUAGUUAUGAACAGAGGAGACAUAACAUGAAC (SEQ ID NO: 6)) asillustrated in FIG. 3A.

The second type of sensor, referred to as the B series, possesses a stemthat has been lengthened by one base pair overall and a loop region thatis only 12-nts. Importantly, the B sensors also lack the downstreamrefolding domain to further stabilize the OFF state. The parentaltoehold switch for the B sensors exhibited extremely low leakage inpreliminary measurements in paper-based reactions and provided asizeable ON/OFF ratio of ˜600-fold regulating GFP expression in E. coli.These B sensors all featured the same conserved sequence(GGACUUUAGAACAGAGGAGAUAAAGAUG (SEQ ID NO: 7)) at the top of theirstem-loops as illustrated in FIG. 2B.

Considerations of Sequence Information in Design of the BiomolecularDiagnostics

Evolutionary drift. At the time we began our experiments, few completegenomes for the Zika virus had been reported. In fact, the firstcomplete genome of the strain circulating in the Americas was onlypublished on January 7 in The Lancet (Enfissi et al., 2016). However,previous comparisons of Zika strains do provide information on thedegree of evolutionary drift for the virus. Haddow et al. found that aZika strain isolated in Malaysia in 1966 differed by only 4.3% innucleotide sequence from isolates obtained Micronesia and Cambodia in2007 and 2010, respectively (Haddow et al., 2012). Authors also found≤11.7% nucleotide sequence difference between African and Asian viruslineages, which they argued provided sufficient conserved sequence forgenetic tests for both lineages. More recent studies have shown the rateof mutation of Zika is ˜10-3 nucleotide changes/site/year, which isrelatively high among flaviviruses, but a manageable rate for ourdiagnostic assay (Faria et al., 2016).

Specificity of the NASBA/toehold switch isothermal assay. Since theexperiments are performed at mostly 41° C. and 37° C.,melting-temperature-dependent tuning of primer specificity is notpossible in our assays. The benefit of this temperature limitation isthat our NASBA and toehold switch detection schemes are able to toleratemismatches and compensate for variability in the sequence of the targetRNA molecules. The binding between the toehold switch 32B, our highestperforming sensor, and RNAs from homologous regions in Zika strainsisolated from Africa (Uganda, Nigeria, Senegal) and Asia (Malaysia,Cambodia, French Polynesia) were analyzed. All these strains arepredicted to fully activate the toehold sensors even with up to 4-nt(11%) mismatches.

Compensating for evolutionary drift. The above analysis is borne out indata showing that sensor 32B can detect the target sequence from boththe American and African strains of the virus (FIG. 8E). Thisflexibility in sequence detection is balanced with the three combinedlayers of specificity in our biomolecular approach. This includes theextensive in silico screening of NASBA primers and toehold switchsequences to limit cross-reactivity with off-target sequences and thesingle-base discrimination of NASBACC. The net result is a programmableplatform that can be manufactured to produce diagnostics with both highsequence specificity and the capacity to manage sequence diversity aspathogens evolve. It is also worth mentioning that, in addition toincreasing specificity, NASBACC can be used to remove non-specificsequences from samples as well as aid in the discovery mutations in thetarget regions.

Integration with signature erosion analysis tools. Software such asBioVelocity (Sozhamannan et al., 2015) and TOPSI (Vijaya Satya et al.,2010) are adept at determining conserved sequence regions acrossmultiple genomes and eliminating those shared with other pathogens orhumans. Using these valuable tools, a set of specific sites for NASBApriming and toehold switch binding can be generated and then subjectedto the same screening by toehold secondary structure and NASBA primercharacteristics described in this work.

Freeze-Dried NASBA.

For freeze-dried NASBA experiments, Enzyme Mix was lyophilizedseparately from the other components. The solution containing reactionbuffer, nucleotide mix, RNase inhibitor, and primers was reconstitutedin 15% DMSO, while the Enzyme Mix was reconstituted in nuclease-freewater.

Freeze-Dried CRISPR/Cas9 Nuclease Assay.

Reactions were performed in a 30 j·tl volume of 1×Cas9 Nuclease ReactionBuffer (NEB #M03865) containing 30 nM of guide RNA (gRNA), 30 nM of Cas9Nuclease (S. pyogenes, NEB #M03865), and 3 nM of substrate DNA(pAG_TS1_KS001 plasmid). Six gRNA sequences targeting the lacZ gene(Doench et al., 2014) inserted into plasmid pAG_TS1_KS001 were used forthe CRISPR/Cas9 freeze-dried assay. All components except substrate DNAwere first combined in a 27 μl reaction volume and incubated for 10minutes at 25° C. to allow Cas9+gRNA to form duplexes. For freshreactions, 3 μl of a 30 nM solution of substrate DNA was added to thesolution. For freeze-dried reactions, the 27 μl solution was lyophilizedovernight and reconstituted with 30 j·tl of a solution containing 3 nMof substrate DNA. After the addition of substrate DNA, the solution wasincubated for 1 h at 37 C and run on a 1% agarose gel for fragmentanalysis.

Care and Use of Macaques at the Wisconsin National Primate ResearchCenter.

All Indian-origin rhesus macaque monkeys from which plasma was isolatedwere cared for by the staff at the Wisconsin National Primate ResearchCenter (WNPRC) in accordance with the regulations and guidelinesoutlined in the Animal Welfare Act and the Guide for the Care and Use ofLaboratory Animals and the recommendations of the Weatherall report.This study was approved by the University of Wisconsin-Madison GraduateSchool Institutional Animal Care and Use Committee (Animal Care and UseProtocol Number G005401). For all procedures (i.e., physicalexamination, virus inoculation, blood and swab collection), animals wereanesthetized with an intramuscular dose of ketamine (10 ml/kg). Bloodsamples were obtained using a vacutainer system or needle and syringefrom the femoral or saphenous vein.

Zika Virus Stock Production for Macaque Infection.

ZIKV strain H/PF/2013 (GenBank accession number: KJ776791), originallyisolated from a 51-year-old female in France returning from FrenchPolynesia with a single round of amplification on Vero cells, wasobtained from Xavier de Lamballerie (European Virus Archive, MarseilleFrance). Virus stocks were prepared by inoculation onto a confluentmonolayer of C6/36 mosquito cells. A single harvest of virus with atiter of 1.26×10⁶ PFU/ml for the Asian-lineage (equivalent to 1.43×10⁹vRNA copies/ml) was used.

Zika Virus Challenge of Macaques, Plasma Collection and Processing.

The virus stock was thawed, diluted in PBS to the appropriateconcentration for each challenge, and loaded into a 1 ml syringe thatwas kept on ice until challenge. Animals were anesthetized as describedabove, and 1 ml of inocula was administered subcutaneously over thecranial dorsum. At the conclusion of the procedure, animals were closelymonitored by veterinary and animal care staff for adverse reactions andsigns of disease. Fresh plasma and PBMC were isolated from EDTA-treatedwhole blood by Ficoll density centrifugation at 1860 rcf for 30 min. Theplasma layer was collected and centrifuged for an additional 8 min at670 rcf to remove residual cells. The supernatant plasma was thenfiltered over a 0.45 μm syringe filter. Collected plasma was diluted1:10 in nuclease free water. Diluted samples were heated to 95 C for twominutes and immediately added to a NASBA reaction as described above.NASBA was run for three hours.

Example 2

Cas9 Interferes with T7-Mediated RNA Production.

RNA can be produced in vitro from a DNA template containing the T7promoter sequence (5′-TAATACGACTCACTATAGGG-3′ (SEQ ID NO: 768)). If theDNA template has viable CRISPR-Cas9 target sites, addition of Cas9+gRNAcomplex to the in vitro RNA production reaction leads to the productionof truncated RNA product.

In FIG. 11, RNA was produced from a DNA template using NEB's HiScribe™T7 Quick High Yield RNA Synthesis Kit. In lane 1, Cas9 without a gRNAwas added to the reaction. In lanes 2 and 3, Cas9+gRNA that target theLacZ gene at positions 717 (gRNA: cttcagcctccagtacagcg (SEQ ID NO: 769))and 360 (gRNA: gttcccacggagaatccgac (SEQ ID NO: 770)) was added to thereaction. Truncated RNA products were produced in lanes 2&3, andfull-length RNA only in lane 1. Traces were generated using aBioAnalyzer (Agilent).

Cas9 can be Freeze-Dried and Remain Active.

It was next tested whether guide RNA targeting the LacZ sequencecontained in the LacZ gene would remain active after being freeze-dried.In particular, a reaction containing Cas9+gRNA complex in Cas9 buffer(NEB #m0386) was freeze dried and re-hydrated with a solution containing3 nM of template DNA. The template DNA is a supercoiled plasmidcontaining the LacZ gene.

In FIGS. 9A-9B, the sequence of 6 gRNA is listed and the gel imageresulting nuclease reaction is shown. Nuclease activity was maintainedfor all gRNA target sequences, and some gRNA (#1, 2, 3, 4, 5) showedincrease activity following the freeze-drying process).

Cas9 without Guide RNA does not Interfere with NASBA.

The presence of Cas9 nuclease alone does not interfere with NASBAreactions. The non-reactivity of NASBA reactions to Cas9 nucleases wasdemonstrated by adding Cas9 nuclease and Cas9 buffer to a NASBAreaction. Since the stability of thermal Cas9 has not been demonstratedabove 37° C., the NASBA reaction was performed at 37° C.

FIG. 12 shows the RNA product from a NASBA reaction (left) and a NASBAreaction with added Cas9, Cas9 buffer, but with no guide RNA (right).Both RNA produces are of the same quality/length. Traces were generatedusing a BioAnalyzer (Agilent).

Cas9 with a gRNA Targeting a Site Lacking a PAM Site does not Interferewith NASBA.

A key aspect of this invention is that a single base mutation affectinga PAM site will present Cas9 from binding/cleaving template DNA. Todemonstrate this, a guide RNA with the 20-bp spacer sequence neg4-noGG(neg4-noGG TTTCAAGAATGGAAAACATC (SEQ ID NO: 771)) was designed to behomologous a region of the American strain (GenBank: KU312312) of ZikaRNA, but at a location that lacks a PAM site (ATG): neg4-noNGG, Loc=2621of GenBank: KU312312, sequence:

(SEQ ID NO: 772) gegggatctcctagTTTCAAGAATGGAAAACATCATGtggagatcagta gaa.

For comparison, another guide RNA sequence with the spacer sequence pos4(pos4: GATCTCCTCTGTTTCAAGAA (SEQ ID NO: 773)) was designed near a PAMsite (TGG) to cut the template DNA and interfere with NASBAamplification: pos4, Loc=2610 of GenBank: KU312312, sequence:

(SEQ ID NO: 774) agatggtatctgcggGATCTCCTCTGTTTCAAGAATGGaaaacatcatg tgga.

FIG. 13 depicts the resulting RNA tract of the NASBA amplificationreaction as quantified on a BioAnalyzer. The “pos4” gRNA cuts theintermediate template DNA and results in a shorter RNA product comparedwith the “neg4-noNGG” gRNA (66 bp vs. 148 bp).

Cas9 with a gRNA that Targets Reverse-Transcribed RNA Interferes withNASBA.

This is demonstrated in FIGS. 8A-8E.

Cas9 can Interfere with NASBA Amplification when Using Low ReverseTranscription (RT) Primers Concentration of 3 nM or Less.

The amount of template DNA that is generated during thereverse-transcription step of a NASBA reaction has to remain low. Usingthe conditions detailed above herein (250 nM final concentration ofCas9+gRNA), it was found that the amount of reverse transcription primerpresent in the NASBA has to be 3 nM or lower in order to efficientlycleave any intermediate template DNA generated during a NASBA reaction.A final concentration of 1 nM is preferable.

FIG. 14 depicts the RNA product generated from three reactionscontaining 1 nM, 3 nM, or 10 nM of NASBA primers. The guide RNA with thespacer sequence TGGAGTCCCGCTGCTAATGA (SEQ ID NO: 775) was designed totarget the African strain (GenBank: KF268950) of the Zika virus. Theexpected size following a successful Cas9 cleavage is 50 base pairs(bp). The full-length, uncut RNA is 200 bp. 8gRNA, Loc=7208 of (GenBank:KF268950)

Sequence:  (SEQ ID NO: 776)ttatgcatgggacttTGGAGTCCCGCTGCTAATGATGGgttgctactca caat

Table Showing the PAM Site Creation/Annihilation Following a RandomMutation (Table 4).

This table shows all the possible outcomes of a random mutation, where aPAM site can be created or annihilated.

Algorithm to Detect Diverging PAM Sites Between Two Strains.

List of PAM sites that differ between the American-African strains (572,FIGS. 8A-8E): see Table 5. Each gRNA sequence in Table 5 provides the30-nt region immediately 5′ to the PAM sequence in the last column. Togenerate the full sgRNA sequence used, the 20 bases adjacent to the 3′end of each gRNA sequence column are identified, and the followingsequence is appended to the 3′ end of that 20-base sequence (an exampleis shown in paragraph 000145):

(SEQ ID NO: 789) 5′-GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTT-3′. sgRNA sequence: Region 8 (8gRNA) +crRNA/tracrRNA (SEQ ID NO: 1) TGGAGTCCCGCTGCTAATGAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTT.

The present invention has been presented by way of illustration and isnot intended to be limited to the disclosed embodiments. Accordingly,those skilled in the art will realize that the invention is intended toencompass all modifications and alternative arrangements within thespirit and scope of the invention as set forth in the appended claims.

TABLE 2  Sequences of NASBA Primers Used for Zika RNA AmplificationToehold Switch Sensor SEQ A BNASBA Primers for Zika Virus from the Americas (KU312312) ID Seriesseries Forward SEQ ID NO: Reverse NO: 1A  25BAATTCTAATACGACTCACTATAGGGAGAAG 8 GCCCAGCTAAAGACTTGGGT 32GCAGTGATCTAGGCTACTGGA ATGA 2A  26B AATTCTAATACGACTCACTATAGGGAGAAG 9CATCCAGTGATCCTCGTTCA 33 GGTGCCAGAGTTGTGTGTACA 3A  27BAATTCTAATACGACTCACTATAGGGAGAAG 10 CCTGTCCTCGGTTCACAATCAA 34GGCACAGTGGGATGATCGTTA 4A  28B AATTCTAATACGACTCACTATAGGGAGAAG 11AATCTCTGTGGACCTCTCCA 35 GCGGGATCTCCTCTGTTTCAA 5A  29BAATTCTAATACGACTCACTATAGGGAGAAG 12 GAGGCCAACAATTCCGACACTA 36GCCATCACTGGGTCTCATCAA 6A  30B AATTCTAATACGACTCACTATAGGGAGAAG 13CTGTCCTCGGTTCACAATCA 37 GAATGCTGTCAGTTCATGGCTCCCA 7A  31BAATTCTAATACGACTCACTATAGGGAGAAG 14 CCAGAACCTTGGATCGTTCA 38GATGGTCTCTTCCTGGTTGTGGA 8A  32B AATTCTAATACGACTCACTATAGGGAGAAG 15CCATCCACAACAGGGTTCTTCA 39 GGACCCTAATAGTGGCCATCA 9A  33BAATTCTAATACGACTCACTATAGGGAGAAG 16 CAGCCCTGGGATCAAGTACATG 40GGTTTGGTATGGGCAAAGGGA TA 10A 34B AATTCTAATACGACTCACTATAGGGAGAAG 17GCCCATACCAAACAACACTCCA 41 GGCCATCTATGCTGCCTTGACAA 11A 35BAATTCTAATACGACTCACTATAGGGAGAAG 18 GCTTAGCCAGGTCACTCATTGA 42GGTGATTCTGCTCATGGTGCA 12A 36B AATTCTAATACGACTCACTATAGGGAGAAG 19AAGTTGGCGCCCATCTCTGAAA 43 GGTTTGTTCCAAGCGTGAGGA 13A 37BAATTCTAATACGACTCACTATAGGGAGAAG 20 GTTCTTTCCTGGGCCTTATCTC 44GAGATCAACCACTGCAAGCGGAA CA 14A 38B AATTCTAATACGACTCACTATAGGGAGAAG 21CCTTCTTGACTCCCTAGAACCA 45 GAGTGGTTCCACGACATTCCA 15A 39BAATTCTAATACGACTCACTATAGGGAGAAG 22 ATCTCTCTGTCATGTGTCCTGG 46GTGGACGCCAGAGTTTGTTCAGA CA 16A 40B AATTCTAATACGACTCACTATAGGGAGAAG 23TCTGAACAAACTCTGGCGTCCA 47 GGCCGGAATAACCTACACAGA 17A 41BAATTCTAATACGACTCACTATAGGGAGAAG 24 GCCCAGCTAAAGACTTGGGTAT 48GGGCTACTGGATTGAGAGTGAGA GA 18A 42B AATTCTAATACGACTCACTATAGGGAGAAG 25TGTTCTCTCCAACCATCCGA 49 GCAGCCAGAATTGCATGTGTCCTCA 19A 43BAATTCTAATACGACTCACTATAGGGAGAAG 26 GCTCTGCAACCAGTTAGTCA 50GGGAGCGGACAAGTTGTCACTTA 20A 44B AATTCTAATACGACTCACTATAGGGAGAAG 27ATCTTCCCAGGCTTGCTTGA 51 GGTGCTCGGTGGACTTCTCAAAGAA 21A 45BAATTCTAATACGACTCACTATAGGGAGAAG 28 TGCCATTCGTTTGAGCCTATCC 52GAGTGGTGCAACTCATTCGGA CA 22A 46B AATTCTAATACGACTCACTATAGGGAGAAG 29GCAGTGGTTGATCTCAGAGA 53 GCAATACCAGAGAGGGCTACA 23A 47BAATTCTAATACGACTCACTATAGGGAGAAG 30 CGCAGGTCAATGTCCATTGAGA 54GAGTAGGTCTTCTGGGCTTGA 24A 48B AATTCTAATACGACTCACTATAGGGAGAAG 31CCACTCTTGTGTGTCCTTCCTA 55 GGCTCAAACGAATGGCAGTCA Toehold Switch SensorNASBA Primers for MR 766 Zika Virus (AY632535) A Series B series ForwardReverse 1A  25B 2A  26B 3A  27B AATTCTAATACGACTCACTATAGGGAGAAGCCTGTCCTCGGTTCACAATCAA GGCACAGTGGGATGATCGTTA  (SEQ ID NO: 58)(SEQ ID NO: 56) 4A  28B 5A  29B 6A  30B 7A  31B 8A  32BAATTCTAATACGACTCACTATAGGGAGAAG  CCATCCACAACGGGATTCTTCAGACTCTGATAGTAGCTATCA  (SEQ ID NO: 59) (SEQ ID NO: 57) 9A  33B 10A 34B11A 35B 12A 36B 13A 37B 14A 38B 15A 39B 16A 40B 17A 41B 18A 42B 19A 43B20A 44B 21A 45B 22A 46B 23A 47B 24A 48B

TABLE 3 Exemplary Materials for Portable Electronic Reader total $:244.238 total Vendor quantity price price item # description Adafruit 124.95 24.95 50 Arduino Uno R3 (Atmega328 - assembled) Adafruit 1 19.9519.95 2078 Adafruit PowerBoost 500 Shield - Rechargeable 5 V PowerShield Adafruit 1 12.5 12.5 2011 Lithium Ion Battery - 3.7 v 2000 mAhAdafruit 1 19.95 19.95 1141 Adafruit Assembled Data Logging shield forArduino Adafruit 1 7.95 7.95 102 SD/MicroSD Memory Card (4 GB SDHC)Adafruit 16 6.26 100.16 1980 Adafruit TSL2591 High Dynamic Range DigitalLight Sensor Sparkfun 3 2.8 8.4 PRT-12702 SparkFun SolderableBreadboard - Mini Digi-Key 2 0.49 0.98 A19473-ND CONN HEADER VERT9POS.100 TIN Digi-Key 2 0.643 1.286 A19476-ND CONN HEADER VERT 13POS.100TIN Digi-Key 2 1.21 2.42 A31001-ND CONN RECEPT 9POS 28AWG MTA100Digi-Key 2 1.93 3.86 A30954-ND CONN RECEPT 13POS 28AWG MTA100 Digi-Key20 0.2246 4.492 36-621-ND BRACKET RT ANG MOUNT 4-40 STEEL, for readerassembly McMaster-Carr 1 2.36 2.36 90760A005 Zinc Plated Steel NarrowHex Nut 4-40 Thread Size, 3/16″ Wide, 1/16″ High, for reader assemblyMcMaster-Carr 1 6.74 6.74 8505K11 Black Acrylic, for readerMcMaster-Carr 2 8.04 16.08 92095A453 M2 screws, for attaching sensorsMcMaster-Carr 1 1.04 1.04 90592A004 M2 nuts, for attaching sensorsInventables 1 4.84 4.84 23876-35 Clear acrylic, for bottom half ofcassette Inventables 1 6.28 6.28 24112-04 Black acrylic, for top half ofcassette

TABLE 4 Probabilities of PAM Site Disruption From Single Point MutationsA. Summary of the effect of single point mutations 12 PAM sites 4 doublePAM sites 32 PAM site created 12 double PAM site created 32 PAM sitedestroyed 12 double PAM site destroyed 4 PAM site inverted Each mutationhas a 23% probability (44/192) of creating a new PAM site, a 23%probability (44/192) of destroying and existing PAM site, and a 2%probability (4/192) of inverting the orientation of an existing PAMsite. Overall, any given point mutations has a 48% probability (92/192)of disrupting an existing PAM site. B. Detailed list of all single pointmutations on every 3-bp sequences. Center letter: A Center letter: CLast Last First A C G T First A C G T A AAA ACA AAC ACC AAG ACG AAT ACTA ACA ACA ACC AAC ACG AAG ACT AAT AGA AGC AGG AGT AGA AGC AGG AGT ATAATC ATG ATT ATA ATC ATG ATT C CAA CCA CAC CCC CAG CCG CAT CCT C CCA CAACCC CAC CCG CAG CCT CAT CGA CGC CGG CGT CGA CGC CGG CGT CTA CTC CTG CTTCTA CTC CTG CTT G GAA GCA GAC GCC GAG GCG GAT GCT G GCA GAA GCC GAC GCGGAG GCT GAT GGA GGC GGG GGT GGA GGC GGG GGT GTA GTC GTG GTT GTA GTC GTGGTT T TAA TCA TAC TCC TAG TCG TAT TCT T TCA TAA TCC TAC TCG TAG TCT TATTGA TGC TGG TGT TGA TGC TGG TGT TTA TTC TTG TTT TTA TTC TTG TTT Centerletter: G Center letter: T Last Last First A C G T First A C G T A AGAAAA AGC AAC AGG AAG AGT AAT A ATA AAA ATC AAC ATG AAG ATT AAT ACA ACCACG ACT ACA ACC ACG ACT ATA ATC ATG ATT AGA AGC AGG AGT C CGA CAA CGCCAC CGG CAG CGT CAT C CTA CAA CTC CAC CTG CAG CTT CAT CCA CCC CCG CCTCCA CCC CCG CCT CTA CTC CTG CTT CGA CGC CGG CGT G GGA GAA GGC GAC GGGGAG GGT GAT G GTA GAA GTC GAC GTG GAG GTT GAT GCA GCC GCG GCT GCA GCCGCG GCT GTA GTC GTG GTT GGA GGC GGG GGT T TGA TAA TGC TAC TGG TAG TGTTAT T TTA TAA TTC TAC TTG TAG TTT TAT TCA TCC TCG TCT TCA TCC TCG TCTTTA TTC TTG TTT TGA TGC TGG TGT

TABLE 5  Suitable sites in the African, Asian, and American Zika virusgenomes for CRISPR complex cleavage. American-African NASBACC genotypingTarget SEQ ID PAM- Strain Position strand gRNA-sequence NO: site African302 −1 TTTTTCCCCACAGAACCCCATCTGTTGATG 60 AGG African 406 1ATGTTGAGAATAATCAATGCTAGGAAGGAG 61 AGG African 433 −1TAGTCAGCAGGAGACCAATGATTCCGATGC 62 TGG African 469 −1CACTTCCACGTCTGGTAATCTCCGCTGCCA 63 TGG African 487 −1CCAAGTACATGTAGTATGCACTTCCACGTC 64 TGG African 517 1CGTGGAAGTGCATACTACATGTACTTGGAC 65 AGG African 547 −1GGCATTTGTTAACTCCCAAGTTGGTAGCAA 66 AGG African 578 −1CACATGTGCCCGAGATCCATGATCTGTACA 67 TGG African 595 1AACAAATGCCATGTACAGATCATGGATCTC 68 GGG African 839 −1TTCCTAAATATCCAGTTTTCAACCTTGATC 69 AGG African 842 1AATCAAGAGAATACACGAAGCACCTGATCA 70 AGG African 871 1AAGGTTGAAAACTGGATATTTAGGAACCCC 71 GGG African 874 −1AGGCAATGGCAACAGCTGCGAGCGCAAACC 72 CGG African 904 −1CTTTTTGGCTCGTCGAGCTTCCCAAAAGCC 73 AGG African 1036 −1AACCTCCATGTTCCAAGACGACATCAACCC 74 AGG African 1075 −1TGTCAACTGTTGGCTTGTCCTGTGCCATAA 75 CGG African 1121 1CAACAGTTGACATAGAGTTGGTCACGACAA 76 CGG African 1141 −1TTGATGCCTCATAACAGTAGGATCTTACCT 77 CGG African 1243 −1TGTCCACCAATGTTCTTTTGCACACATATT 78 GGG African 1244 −1CTGTCCACCAATGTTCTTTTGCACACATAT 79 TGG African 1262 1CAGACACCCAATATGTGTGCAAAAGAACAT 80 TGG African 1285 1AGAACATTGGTGGACAGAGGTTGGGGAAAT 81 GGG African 1330 −1TCCCAGTCATCTTCTTGGAACACGTGAACT 82 TGG African 1478 1ATGAAACTGACGAAAACAGAGCGAAAGTCG 83 AGG African 1562 1TAGGACTTGATTGTGAACCAAGGACAGGCC 84 TGG African 1594 −1CTTTGTGCACCAACCAGTGCTTGTTGTTCA 85 TGG African 1643 −1CCGGTATCTGCCCCAGCATGCCAAGGCAAT 86 GGG African 1691 1CAGATACCGGAACTCCACACTGGAACAACA 87 AGG African 1694 1ATACCGGAACTCCACACTGGAACAACAAGG 88 AGG African 1723 −1CTAGAACAACGACGGTTTGCCTCTTGGCGT 89 GGG African 1724 −1CCTAGAACAACGACGGTTTGCCTCTTGGCG 90 TGG African 1741 −1CGGCTCCTTCCTGGCTCCCTAGAACAACGA 91 CGG African 1757 1AGAGGCAAACCGTCGTTGTTCTAGGGAGCC 92 AGG African 1760 −1CCAGCAAGAGCCGTGTGAACGGCTCCTTCC 93 TGG African 1771 −1CCTCCAGAGCTCCAGCAAGAGCCGTGTGAA 94 CGG African 1837 −1TGTCCATTTTTAAGCGGCATTTCAAATGGC 95 CGG African 1853 −1CCCTTCAATCTAAGCTTGTCCATTTTTAAG 96 CGG African 1906 −1CAGCTGGGACCTTGGTAAATGTGAACGCTG 97 CGG African 1922 1CCTTGTGCACCGCAGCGTTCACATTTACCA 98 AGG African 1993 −1TGTCCACCGCCATCTGGGCTGGGACCTTGC 99 AGG African 2003 −1AGGGTCTGCATGTCCACCGCCATCTGGGCT 100 GGG African 2008 −1GGGTCAGGGTCTGCATGTCCACCGCCATCT 101 GGG African 2032 −1TGGCGGTTATCAGCCTCCCGACTGGGGTCA 102 GGG African 2033 −1TTGGCGGTTATCAGCCTCCCGACTGGGGTC 103 AGG African 2062 −1AATTCTCAGTGCTTTCAGTAATCACAGGGT 104 TGG African 2117 −1CCTATGACAATGTAAGAATCCCCAAATGGT 105 GGG African 2210 1GGAGTGGTAGCACCATCGGAAAAGCATTTG 106 AGG African 2248 1GTGAGAGGTGCCAAGAGAATGGCAGTTCTG 107 GGG African 2249 1TGAGAGGTGCCAAGAGAATGGCAGTTCTGG 108 GGG African 2278 1GGGGATACAGCCTGGGACTTCGGATCAGTC 109 GGG African 2279 1GGGATACAGCCTGGGACTTCGGATCAGTCG 110 GGG African 2318 −1AACAGTGATTTGAAAGCTGCTCCAAAAATC 111 TGG African 2378 −1AAACCCAACCACACCAGCAGCGTGCCTATG 112 AGG African 2390 1GGTTCTCACAGATCCTCATAGGCACGCTGC 113 TGG African 2428 −1CTCCCCCCAGGGCCAAGCATGTGAGGGAGA 114 TGG African 2447 1ATGGATCCATCTCCCTCACATGCTTGGCCC 115 TGG African 2471 −1CACCCCACGTCAGCAGAGACAGCCGTGGAG 116 AGG African 2474 1CCCTGGGGGGAGTGATGATCTTCCTCTCCA 117 CGG African 2537 1ACTTCTCAAAAAGAGAAACGAGATGTGGCA 118 CGG African 2630 1CCCCCCGCAGATTGGCAGCAGCAGTCAAGC 119 AGG African 2642 1TGGCAGCAGCAGTCAAGCAGGCTTGGGAAG 120 AGG African 2644 1GCAGCAGCAGTCAAGCAGGCTTGGGAAGAG 121 GGG African 2668 −1ATTTCCACATGATGTTTTCCATTCTTGAAA 122 CGG African 2699 1CAAGAATGGAAAACATCATGTGGAAATCAG 123 TGG African 2792 −1AGCTCATTCACAGGCACTGGCAATCTTTGT 124 GGG African 2864 1AAGCCTGGGGGAAATCATATTTTGTCAGAG 125 CGG African 2878 −1GTGTGTCACCATCGACAACAAAACTGTTGT 126 TGG African 2981 −1TCTTCTCTAACCTTGAGCCAAACACTGGTG 127 TGG African 2986 −1AGTAGTCTTCTCTAACCTTGAGCCAAACAC 128 TGG African 3032 −1TTTCCCTTAACAGCTGTTCCTATGACGGCT 129 GGG African 3070 −1TTTCAATCCAGTAGCCCAGGTCACTGTGGG 130 CGG African 3073 −1CACTTTCAATCCAGTAGCCCAGGTCACTGT 131 GGG African 3074 −1TCACTTTCAATCCAGTAGCCCAGGTCACTG 132 TGG African 3080 1TTAAGGGAAAGGAGGCCGCCCACAGTGACC 133 TGG African 3083 −1TCATTCTTTTCACTTTCAATCCAGTAGCCC 134 AGG African 3251 −1GCTTGAGTTCTGTAACCCTCTCTAGTGTTG 135 TGG African 3317 −1TGAACCTTGGTGCCTGGACATTCCTCAAAC 136 CGG African 3340 −1TAGTTCCGCATGTCTCCTCCACGTGAACCT 137 TGG African 3542 1AGAGCAACTTAGTGAGGTCAATGGTGACAG 138 CGG African 3556 −1GCACTCCAAGAGAGAAGTGGTCCATGTGAT 139 CGG African 3668 1TCATTATGAGCACATCAATGGCAGTGCTGG 140 TGG African 3676 −1AGTCACTCATTAAAAATCCTCCCAGGATCA 141 TGG African 3764 1CCTTCGCAGAAATGAACACTGGAGGAGATG 142 TGG African 3779 1ACACTGGAGGAGATGTGGCTCACTTGGCAT 143 TGG African 3811 −1AATTAGCTCTGAAAATAAAGGAGACCAGCA 144 AGG African 3823 −1CACGAGGTGTCCAATTAGCTCTGAAAATAA 145 AGG African 3872 −1GAGATTGCAGTTTGCAAAAGACACGAAGCC 146 AGG African 3929 −1GCCAACCAGGCCAAAGCAAATCCATTGACG 147 AGG African 3976 −1TTGCCAGAGCAATGTTGTCAGTGCGTGGCA 148 CGG African 4058 1CCCGAGGTACACTGCTCGTGGCATGGAGAG 149 CGG African 4099 −1GGTTCTTCTTCACACTACCTTTCCCTTTCA 150 GGG African 4102 1TGTGGAGGGTTTATGCTCCTCTCCCTGAAA 151 GGG African 4130 −1GCAGTCAATCCCAAGGCCATGACAAATGGC 152 AGG African 4409 1TTGAAAGAGCAGGTGACATCACATGGGAAA 153 AGG African 4639 −1TGGTCTCTCCTTTTTTCACTTCTTTGGGAG 154 CGG African 4672 1AAAGAAGTGAAAAAAGGAGAGACCACAGAT 155 GGG African 4673 1AAGAAGTGAAAAAAGGAGAGACCACAGATG 156 GGG African 4696 −1CTCCAACCTGTGTTGAACCCAGCAGTCTGC 157 GGG African 4697 −1ACTCCAACCTGTGTTGAACCCAGCAGTCTG 158 CGG African 4703 1GGGTATACAGAGTGATGACCCGCAGACTGC 159 TGG African 4715 1TGATGACCCGCAGACTGCTGGGTTCAACAC 160 AGG African 4754 −1GCAGCTCCTTTTGTGACGTGCCACATGGTG 161 TGG African 4786 1ATGTGGCACGTCACAAAAGGAGCTGCACTG 162 AGG African 4819 1AGCGGTGAAGGGAGACTTGATCCATACTGG 163 GGG African 4820 1GCGGTGAAGGGAGACTTGATCCATACTGGG 164 GGG African 4852 1GATGTCAAGCAGGACTTAGTGTCATACTGT 165 GGG African 4865 1ACTTAGTGTCATACTGTGGGCCTTGGAAGT 166 TGG African 4924 1GTGCAGCTCTTGGCAGTACCCCCCGGAGAG 167 AGG African 4925 1TGCAGCTCTTGGCAGTACCCCCCGGAGAGA 168 GGG African 4933 −1TGAATATTCCAGGCAGAGTCTGAATGTTTC 169 TGG African 5008 −1TGTCTAGGATCGGGGATCCTGAAGTTCCTG 170 CGG African 5026 −1CTATCACTCTTCCGCATTTGTCTAGGATCG 171 GGG African 5027 −1CCTATCACTCTTCCGCATTTGTCTAGGATC 172 GGG African 5111 1AGAATGGAAGCTATGTTAGTGCCATAACCC 173 AGG African 5126 1TTAGTGCCATAACCCAGGGAAAGAGGGAGG 174 AGG African 5135 1TAACCCAGGGAAAGAGGGAGGAGGAGACTC 175 CGG African 5158 −1GGACAGTTAGCTGCTTCTTCTTCAGCATCG 176 AGG African 5186 1CGATGCTGAAGAAGAAGCAGCTAACTGTCC 177 TGG African 5189 −1CTAGTCTTTCCGGCTCCTGGATGCAGATCC 178 AGG African 5209 −1CTATTTCAGGAAGAACTCTCCTAGTCTTTC 179 CGG African 5276 1CCATAAAAAAGAGACTCCGCACAGTGATTT 180 TGG African 5330 1CTGAGATGGAGGAAGCCTTGAGAGGACTTC 181 CGG African 5371 1ATGACAACAGCAGTTAACGTCACCCACTCT 182 GGG African 5416 −1TAGGGACTCTGATGGGTTGTAATAGGCGTG 183 AGG African 5423 −1TTGTAATTAGGGACTCTGATGGGTTGTAAT 184 AGG African 5434 −1TGATGTAGAGATTGTAATTAGGGACTCTGA 185 TGG African 5489 −1GATATGTATCCTCTTGCAGCTATACTTGAG 186 GGG African 5678 −1CTTGGAACGAACCAAACTGTTTTCCCAGAA 187 TGG African 5680 1TCAGGCTTTGATTGGGTGACAGACCATTCT 188 GGG African 5737 −1GTATGACCCGCTTTCCAGCCTTTGTCAGAC 189 AGG African 5773 1AAGGCTGGAAAGCGGGTCATACAACTCAGC 190 AGG African 5875 1TCAGAGATGGGCGCGAATTTCAAAGCTGAC 191 CGG African 5876 1CAGAGATGGGCGCGAATTTCAAAGCTGACC 192 GGG African 5941 1ATACTTGATGGTGAGAGAGTCATCTTGGCT 193 GGG African 6005 −1CCATACATGTACTCATCTCCAGGTTTGTTA 194 GGG African 6055 −1TTGCTTCAAGCCAGTGTGCATGGTCTTCAT 195 CGG African 6136 1CTCCAGGATGGCCTCATAGCCTCGCTCTAC 196 CGG African 6140 −1TCAATGGCAGCTACCTTATCGGCCTCAGGC 197 CGG African 6152 1TAGCCTCGCTCTACCGGCCTGAGGCCGATA 198 AGG African 6236 −1GATGCAACCTGATAGGCTAGCCAAACGGGA 199 AGG African 6403 1AGAGTGCTCAAACCAAGATGGATGGATGCG 200 AGG African 6404 1GAGTGCTCAAACCAAGATGGATGGATGCGA 201 GGG African 6418 −1ATTCTTTGAACGACTTCAGGGCAGCATGAT 202 CGG African 6457 −1CCATTACTCCTAAAGCCACTCCTCTTTTCC 203 CGG African 6485 1GGAAAAGAGGAGTGGCTTTAGGAGTAATGG 204 AGG African 6520 1CTGGGAACATTGCCAGGACACATGACAGAG 205 AGG African 6587 1TGCGAGCAGAGACTGGAAGCAGGCCTTACA 206 AGG African 6661 1CTCTTAGGCTTGTTGGGAACAGTTTCGTTG 207 GGG African 6829 −1TGTCCTGGGGAGATCTTTGCTTCTCTGGCT 208 CGG African 6881 1AGGACAACCAGATGGCAATCATCATCATGG 209 TGG African 6887 1ACCAGATGGCAATCATCATCATGGTGGCAG 210 TGG African 6989 1TAATGGGAAGGAGAGAAGAAGGAGTAACTA 211 TGG African 7033 −1TGAGAGTTGTCAGTGCGGCATAGATAGCCC 212 AGG African 7048 −1GGACGGCTGGGGTGATGAGAGTTGTCAGTG 213 CGG African 7082 1CAACTCTCATCACCCCAGCCGTCCAACACG 214 CGG African 7206 1AT-GGGACTTTGGAGTCCCGCTGCTAATGA 215 TGG African 7358 −1CAATGTCAGTTACCACTATTCCATCCACAA 216 CGG African 7526 −1ATTTGTTTGGAGAACCTTCCCACAAGGTGG 217 AGG African 7580 −1GGTAACTTCCTCTGAAGATGTTGCACAGTG 218 AGG African 7611 −1GTCACTGTATAAATAAGAGAAGCGCCTGCC 219 AGG African 7656 −1TCTCCCGTTCCACCTCCACGTCTCTTGACT 220 AGG African 7677 1CTGGCCTAGTCAAGAGACGTGGAGGTGGAA 221 CGG African 7716 −1GAGTAGAACTCCAGGGCCGACATCTGATTC 222 AGG African 7779 1AAAAGTCAGGCATCACTGAAGTGTGTAGAG 223 AGG African 7817 −1CGCTTCCCCGGGATACAGCATGTCCTCCTG 224 TGG African 7835 1GGAGTGGCCACAGGAGGACATGCTGTATCC 225 CGG African 7836 1GAGTGGCCACAGGAGGACATGCTGTATCCC 226 GGG African 7890 −1CTGCCACATCCGAGGTCAACAACCTTTCCA 227 TGG African 7908 −1TAATAGCTCCAACCCCCTCTGCCACATCCG 228 AGG African 7959 1GCTATTATGCCGCCACCATCCGGAAAGTGC 229 AGG African 7962 1ATTATGCCGCCACCATCCGGAAAGTGCAGG 230 AGG African 7980 1GGAAAGTGCAGGAGGTGAAAGGATACACAA 231 AGG African 7994 −1AGCTTTGCACCAGCATGGGTTCTTCATGAC 232 CGG African 8081 −1CTATGTCACACAGCAAGGTATCACACGGCT 233 CGG African 8096 −1TAGATGATGACTCACCTATGTCACACAGCA 234 AGG African 8157 −1TCAAGCCAGTCCCCCACCATAGAGAGCACT 235 CGG African 8193 1CTATGGTGGGGGACTGGCTTGAGAAAAGAC 236 CGG African 8195 1ATGGTGGGGGACTGGCTTGAGAAAAGACCG 237 GGG African 8196 1TGGTGGGGGACTGGCTTGAGAAAAGACCGG 238 GGG African 8211 1TTGAGAAAAGACCGGGGGCCTTCTGTATAA 239 AGG African 8262 −1CTGACTAATCCTCCCCCATACCTACGTTGC 240 AGG African 8315 −1TTGCTCCAGAGACCCAATACATCTCATGTG 241 TGG African 8391 −1ACTGGCCTCCTGGGACCATCCATGCGTCCC 242 AGG African 8445 −1CAGCTTGCCACAGCTCGTGTGCCCGAGCCG 243 AGG African 8448 1TGAAATATGAGGAAGATGTGAACCTCGGCT 244 CGG African 8493 1TGGCAAGCTGTGCTGAAGCTCCCAACATGA 245 AGG African 8585 −1CTTGTGTGGGGGCTTCGTAGCTCCCATGGT 246 AGG African 8588 1AACCATCCATACAGGACATGGGCCTACCAT 247 GGG African 8630 −1TTGACAGGAGTCTAACAACCCCATTCACGA 248 GGG African 8631 −1TTTGACAGGAGTCTAACAACCCCATTCACG 249 AGG African 8724 −1GTGTCCACTTTTTCTTTGAAGACTCTTTGT 250 TGG African 8756 −1GGCGAGTGCCTTCTTGGGGATCTGGCACCC 251 TGG African 8787 −1CACAGCCAGGAAGAGACCATGTTCATTGCC 252 TGG African 8817 1CAATGAACATGGTCTCTTCCTGGCTGTGGA 253 AGG African 8823 1ACATGGTCTCTTCCTGGCTGTGGAAGGAGT 254 TGG African 8825 1ATGGTCTCTTCCTGGCTGTGGAAGGAGTTG 255 GGG African 8895 1TCATCAACAAGGTGCGCAGCAATGCAGCAC 256 TGG African 8931 1CAATATTTGAAGAGGAAAAAGAATGGAAGA 257 CGG African 8939 −1CCCAAAACCTTGGATCATTCACAGCCTCCA 258 CGG African 8940 1AAGAGGAAAAAGAATGGAAGACGGCCGTGG 259 AGG African 9105 1AAGGCAGCCGCGCCATCTGGTACATGTGGT 260 TGG African 9116 −1AGAATCCAAGGGCTTCAAACTCCAAGAATC 261 TGG African 9120 1TCTGGTACATGTGGTTGGGAGCCAGATTCT 262 TGG African 9159 −1CCACCTCCTGAGTTTTCTCTTCCCATCCAA 263 TGG African 9239 1AGACTTGGATACATTCTAGAAGAAATGAAT 264 CGG African 9240 1GACTTGGATACATTCTAGAAGAAATGAATC 265 GGG African 9278 −1CAAACTTACTAATGCGGGTGTCCCAGCCAG 266 CGG African 9326 −1TGTGCCCTTCCTCCATTTGGTTGGTAATTA 267 AGG African 9342 1AGAATGAAGCCTTAATTACCAACCAAATGG 268 AGG African 9424 1CAAAGTGGTGAAGGTCCTCAGACCAGCTGA 269 AGG African 9459 1GGAAAACAGTTATGGACATCATTTCAAGAC 270 AGG African 9494 −1CCACTAAGTTGGTAAATGTGTTGAGAGCAT 271 AGG African 9537 −1ATCTCTAACACTTCCTCAGCCTCCATATTC 272 CGG African 9595 −1ATTGCACTGCAACCATCTGGTCACTTTCTC 273 TGG African 9747 1ATGACATGGGAAAAGTTAGGAAAGACACAC 274 AGG African 9795 −1TGCAGCTTGTTGAAATGGTGGGAGCAGAAC 275 GGG African 9855 −1CGGCCAATCAATTCATCTTGGTGGCGGCAA 276 GGG African 9932 −1GCCACATCTGTGCATATGATTTTGCTAGAC 277 AGG African 10014 1ACCTTCGACTGATGGCCAATGCTATTTGTT 278 CGG African 10046 −1CCTTTCCGTGGATTGACCAGGTGGTTCTCC 279 CGG African 10092 1TCCACGGAAAGGGAGAATGGATGACTACTG 280 AGG African 10146 1GAGTGTGGATTGAGGAGAACGACCATATGG 281 AGG African 10185 −1CACCATAAGTCCTCCCTTTTTCCCAGATAG 282 GGG African 10200 1GGACAGACATCCCCTATCTGGGAAAAAGGG 283 AGG African 10223 −1CCCAAGTGGTGCGGGGCCTGTGCCCTATAA 284 GGG African 10224 −1GCCCAAGTGGTGCGGGGCCTGTGCCCTATA 285 AGG African 10232 1GACTTATGGTGTGGATCCCTTATAGGGCAC 286 AGG African 10241 −1TGTCTTTGATGTTCTCAGCCCAAGTGGTGC 287 GGG African 10242 −1GTGTCTTTGATGTTCTCAGCCCAAGTGGTG 288 CGG African 10332 1AAGAAAAATACATGGACTACTTATCCACCC 289 AGG African 10341 −1CCAGGTGTGGACCCTTCCTCACCCAAGTAG 290 CGG African 10350 1ACTTATCCACCCAGGTCCGCTACTTGGGTG 291 AGG American 188 1AACGCGGAGTAGCCCGTGTGAGCCCCTTTG 292 GGG American 229 1AGGCTGCCAGCCGGACTTCTGCTGGGTCAT 293 GGG American 275 1TCTTGGCGATTCTAGCCTTTTTGAGATTCA 294 CGG American 368 1TGGAAATAATAAAGAAGTTCAAGAAAGATC 295 TGG American 452 −1ACCTCCGCTGCCATAGCTGTGGTCAGCAGG 296 AGG American 463 −1CACGTCTAGTGACCTCCGCTGCCATAGCTG 297 TGG American 476 1GCCTCCTGCTGACCACAGCTATGGCAGCGG 298 AGG American 490 1ACAGCTATGGCAGCGGAGGTCACTAGACGT 299 GGG American 530 1ACTATATGTACTTGGACAGAAACGATGCTG 300 GGG American 552 −1TATATAACACTTATTCATCCCCAATGTGGT 301 TGG American 559 1GGGGAGGCCATATCTTTTCCAACCACATTG 302 GGG American 646 1ATGAGCTATGAATGCCCTATGCTGGATGAG 303 GGG American 647 1TGAGCTATGAATGCCCTATGCTGGATGAGG 304 GGG American 719 −1CTAGATCTCCGTGCTTCACCTTTTTTGTGA 305 TGG American 769 −1ACCGCGTTTGCAGCTTCCTAGTGGAATGGG 306 AGG American 772 −1GCGACCGCGTTTGCAGCTTCCTAGTGGAAT 307 GGG American 773 −1TGCGACCGCGTTTGCAGCTTCCTAGTGGAA 308 TGG American 809 1GGAAGCTGCAAACGCGGTCGCAAACCTGGT 309 TGG American 1000 1TACAGCATCAGGTGCATAGGAGTCAGCAAT 310 AGG American 1001 1ACAGCATCAGGTGCATAGGAGTCAGCAATA 311 GGG American 1136 1AGCTGGTTACAACAACAGTCAGCAACATGG 312 CGG American 1196 −1TCAAGGTAGGCTTCACCTTGTGTTGGGCAG 313 CGG American 1357 −1ACTCCAGATTCTCTGGCTGGATGCTCTTCC 314 CGG American 1387 1AAGAGCATCCAGCCAGAGAATCTGGAGTAC 315 CGG American 1391 −1TGCTGGGAGCCATGAACTGACAGCATTATC 316 CGG American 1507 −1CTAGGCTTCCAAACCCCCCCAGGGTGGCTT 317 CGG American 1513 −1CAAGTCCTAGGCTTCCAAACCCCCCCAGGG 318 TGG American 1517 −1CAATCAAGTCCTAGGCTTCCAAACCCCCCC 319 AGG American 1519 1AATTCACCAAGAGCCGAAGCCACCCTGGGG 320 GGG American 1535 −1AGGCCTGTCCTCGGTTCACAATCAAGTCCT 321 AGG American 1619 1CTATGAATAACAAGCACTGGCTGGTTCACA 322 AGG American 1634 −1GCCCCAGCGTGCCAAGGTAATGGAATGTCG 323 TGG American 1712 1GGAACAACAAAGAAGCACTGGTAGAGTTCA 324 AGG American 1742 1AGGACGCACATGCCAAAAGGCAAACTGTCG 325 TGG American 1783 −1CATCCATCTCAGCCTCCAGAGCTCCAGCAA 326 GGG American 1784 −1CCATCCATCTCAGCCTCCAGAGCTCCAGCA 327 AGG American 1817 1GAGCTCTGGAGGCTGAGATGGATGGTGCAA 328 AGG American 1834 −1CCATTTTCAGGCGACATTTCAAGTGGCCAG 329 AGG American 1856 −1ACGCCCTTCAATCTAAGTTTATCCATTTTC 330 AGG American 1928 1GTACTGCAGCGTTCACATTCACCAAGATCC 331 CGG American 1945 1TTCACCAAGATCCCGGCTGAAACACTGCAC 332 GGG American 2068 −1TCTTAGAGTTCTCAGTGCTTTCAGTGATTA 333 CGG American 2174 −1TTTCCAATGGTGCTGCCACTCCTGTGCCAG 334 TGG American 2315 −1AATGATTTGAAAGCTGCTCCAAAGATTTGA 335 TGG American 2482 −1AGTCCACCGAGCACCCCACATCAGCAGAGA 336 CGG American 2519 1ATGTGGGGTGCTCGGTGGACTTCTCAAAGA 337 AGG American 2638 −1CAGAGGAGATCCCGCAGATACCATCTTCCC 338 AGG American 2723 1GATCAGTAGAAGGGGAGCTCAACGCAATCC 339 TGG American 2747 1CAATCCTGGAAGAGAATGGAGTTCAACTGA 340 CGG American 2756 1AAGAGAATGGAGTTCAACTGACGGTCGTTG 341 TGG American 2806 −1TCCAGCCGTGGGGCAGCTCGTTCACAGGCA 342 CGG American 2834 1TGCCTGTGAACGAGCTGCCCCACGGCTGGA 343 AGG American 2891 1GAGCAGCAAAGACAAATAACAGCTTTGTCG 344 TGG American 2921 −1AGAAAGCTGTTCCATGCTCTATGTTTGAGT 345 GGG American 3175 −1TCTCTTCTATTCCATCTGTCCACAATGTGT 346 GGG American 3176 −1CTCTCTTCTATTCCATCTGTCCACAATGTG 347 TGG American 3223 −1TGTGATGGCTGAGTGGCCCAGCTAAAGACT 348 TGG American 3232 1AGTGATCTGATCATACCCAAGTCTTTAGCT 349 GGG American 3259 −1GCCCTTTCATTTGGGTCCTGTAGCCCTCTC 350 TGG American 3268 1CTCAGCCATCACAATACCAGAGAGGGCTAC 351 AGG American 3277 −1GCTCTTCACTGTGCCATGGCCCTTTCATTT 352 GGG American 3278 −1AGCTCTTCACTGTGCCATGGCCCTTTCATT 353 TGG American 3332 −1CATGTTTCCTCCACGTGGACCTTAGTGCCT 354 GGG American 3427 1AGCGGAAGGGTGATCGAGGAATGGTGCTGC 355 AGG American 3428 1GCGGAAGGGTGATCGAGGAATGGTGCTGCA 356 GGG American 3457 1AGGGAGTGCACAATGCCCCCACTGTCGTTC 357 CGG American 3458 1GGGAGTGCACAATGCCCCCACTGTCGTTCC 358 GGG American 3461 −1TCCATTCCATACCAACAGCCATCTTTAGCC 359 CGG American 3577 −1GCACCATGAGCAGAATCACAAGCACTCCAA 360 GGG American 3578 −1TGCACCATGAGCAGAATCACAAGCACTCCA 361 AGG American 3605 1TTGGAGTGCTTGTGATTCTGCTCATGGTGC 362 AGG American 3707 −1GTGGCACCCATCAAAATTGCAAGCTTAGCC 363 AGG American 3740 1AGCTTGCAATTTTGATGGGTGCCACCTTCG 364 CGG American 3850 −1ACGAGGCCAAGGCCAGCAGCATGCTTTCAC 365 GGG American 3851 −1CACGAGGCCAAGGCCAGCAGCATGCTTTCA 366 CGG American 3863 1CTAATTGGACACCCCGTGAAAGCATGCTGC 367 TGG American 3877 −1AGGCGGAGATCGCAGTTTGCAAAAGACACG 368 AGG American 3904 −1TGATGAGAACCATCAGGTCGCCTTCCAAGG 369 CGG American 3905 1CGTGTCTTTTGCAAACTGCGATCTCCGCCT 370 TGG American 3907 −1CATTGATGAGAACCATCAGGTCGCCTTCCA 371 AGG American 4000 −1CCAGTGGTGTCAGAGCAGCCAGGATTGCCA 372 AGG American 4025 1CCTTGGCAATCCTGGCTGCTCTGACACCAC 373 TGG American 4030 1GCAATCCTGGCTGCTCTGACACCACTGGCC 374 CGG American 4031 1CAATCCTGGCTGCTCTGACACCACTGGCCC 375 GGG American 4075 1GTGGCGTGGAGAGCAGGCCTTGCTACTTGC 376 GGG American 4076 1TGGCGTGGAGAGCAGGCCTTGCTACTTGCG 377 GGG American 4148 −1GGGTCGACCAGCCTCACAGCGGTTAGTCCC 378 AGG American 4159 −1CCACGTTGATGGGGTCGACCAGCCTCACAG 379 CGG American 4166 1TCATGGCCCTGGGACTAACCGCTGTGAGGC 380 TGG American 4322 1CAGATATAGAGATGGCTGGGCCCATGGCCG 381 CGG American 4324 −1CCACGTAACTGACAATTAGCAGACCGACCG 382 CGG American 4441 −1CACCACTCTCATCTAGCGCCACATCGAGCC 383 GGG American 4442 −1TCACCACTCTCATCTAGCGCCACATCGAGC 384 CGG American 4480 −1CTCTCATGGGGGGACCGTCATCCTCCACCA 385 GGG American 4501 −1GGACCACCTTGAGTATGATCTCTCTCATGG 386 GGG American 4502 −1AGGACCACCTTGAGTATGATCTCTCTCATG 387 GGG American 4643 1GTGGTGCTCTATGGGATGTGCCTGCTCCCA 388 AGG American 4655 1GGGATGTGCCTGCTCCCAAGGAAGTAAAAA 389 AGG American 4657 1GATGTGCCTGCTCCCAAGGAAGTAAAAAAG 390 GGG American 4658 1ATGTGCCTGCTCCCAAGGAAGTAAAAAAGG 391 GGG American 4741 1ACACAAGTTGGAGTGGGAGTTATGCAAGAG 392 GGG American 4742 1CACAAGTTGGAGTGGGAGTTATGCAAGAGG 393 GGG American 4783 −1GATCAAGTCTCCCTTCACCGCTTCTCAGCG 394 CGG American 4838 1ATCCATACTGGGGAGATGTCAAGCAGGATC 395 TGG American 4879 −1CCAAGAGCTGCACCTCGCTGTGCCCGTCCC 396 AGG American 4882 1GGTCCATGGAAGCTAGATGCCGCCTGGGAC 397 GGG American 4912 −1GGATGTTCCTCGCTCTCTCTCCGGGGGGCA 398 CGG American 4930 1CTCTTGGCCGTGCCCCCCGGAGAGAGAGCG 399 AGG American 4943 −1TCCTTTGTCTTAAATATTCCGGGCAGAGTC 400 TGG American 4954 −1CAATGTCCCCATCCTTTGTCTTAAATATTC 401 CGG American 4985 1TATTTAAGACAAAGGATGGGGACATTGGAG 402 CGG American 5041 1ACTTCAGGATCTCCTATCCTAGACAAGTGT 403 GGG American 5086 1CTTTATGGCAATGGGGTCGTGATCAAAAAT 404 GGG American 5116 1GGGAGTTATGTTAGTGCCATCACCCAAGGG 405 AGG American 5206 1CTAACTGTCTTAGACTTGCATCCTGGAGCT 406 GGG American 5218 −1CTTCACGGACTATTTCAGGAAGAACTCTCC 407 TGG American 5312 1CAACCAGGGTTGTCGCTGCTGAAATGGAGG 408 AGG American 5321 −1GTTGTCATATAACGCACTGGAAGCCCTCTA 409 AGG American 5323 1GTCGCTGCTGAAATGGAGGAGGCCCTTAGA 410 GGG American 5446 −1GGGCCTCATCCATAATATACAGATTATAGT 411 TGG American 5468 1TCCCCAACTATAATCTGTATATTATGGATG 412 AGG American 5548 −1TTCCTGGTGGCGTGGCGGTCATGAAGATGG 413 CGG American 5563 −1GAAATGCGTCACGGGTTCCTGGTGGCGTGG 414 CGG American 5591 1CCACGCCACCAGGAACCCGTGACGCATTTC 415 CGG American 5623 −1AGCTCCAGGCTCTCTCTGGGACTTCCACTT 416 CGG American 5669 1GAGCCTGGAGCTCAGGCTTTGATTGGGTGA 417 CGG American 5710 1GGAAAAACAGTTTGGTTTGTTCCAAGCGTG 418 AGG American 5801 −1ACAAAGTCCCACTCTTGATGTTTTGTTTTC 419 TGG American 5863 −1TGGAATCTATGACACGGTCAGCTTTAAAGT 420 TGG American 5893 −1CATCAAGTATGACCGGCTTTAGGCATCTCC 421 TGG American 5906 1GTGTCATAGATTCCAGGAGATGCCTAAAGC 422 CGG American 5968 −1TGCCTATGCGCCCCCTCCTCTGGGCAGCGC 423 TGG American 5978 −1TTGGGATTCCTGCCTATGCGCCCCCTCCTC 424 TGG American 5980 1CCTGTCACACATGCCAGCGCTGCCCAGAGG 425 AGG American 5981 1CTGTCACACATGCCAGCGCTGCCCAGAGGA 426 GGG American 6007 −1CTCCATACAGATACTCATCTCCAGGTTTGT 427 TGG American 6037 1AAACCTGGAGATGAGTATCTGTATGGAGGT 428 GGG American 6095 −1ATGAGGCCATCTTGGAGGTAAATATTGTCA 429 AGG American 6188 1CAGCCATTGAGGGAGAGTTCAAGCTTAGGA 430 CGG American 6245 1TCATGAAAAGAGGAGATCTTCCTGTTTGGC 431 TGG American 6280 −1TGCCATCAAAGCACCATCTTCTATCTGTGT 432 AGG American 6341 1CCAACAACACCATAATGGAAGACAGTGTGC 433 CGG American 6361 −1TCGGTTTGAGCACTCTTTTCTCTCCGTGTC 434 TGG American 6388 1AGACACGGAGAGAAAAGAGTGCTCAAACCG 435 AGG American 6406 −1ACTTCAGGGCCGCATGATCTGAACAAACTC 436 TGG American 6422 1GGATGGACGCCAGAGTTTGTTCAGATCATG 437 CGG American 6440 1GTTCAGATCATGCGGCCCTGAAGTCATTCA 438 AGG American 6548 −1CTTCCAGTCTCTGCCCGCATGAGCACAGCG 439 AGG American 6559 1GAAGCCATTGACAACCTCGCTGTGCTCATG 440 CGG American 6560 1AAGCCATTGACAACCTCGCTGTGCTCATGC 441 GGG American 6595 −1TCTCTAGGGTCTCCGGCAATTGGGCCGCCG 442 CGG American 6596 1AGACTGGAAGCAGGCCTTACAAAGCCGCGG 443 CGG American 6635 1TGCCGGAGACCCTAGAGACCATTATGCTTT 444 TGG American 6637 1CCGGAGACCCTAGAGACCATTATGCTTTTG 445 GGG American 6806 −1TCTGGCTCAGGTATGAGCACCACCAGCAAT 446 AGG American 6913 −1TTGTTCTCTCCAACCATCCGAGTTCATTGG 447 CGG American 6916 −1TCTTTGTTCTCTCCAACCATCCGAGTTCAT 448 TGG American 6953 −1CCCTCCTCTCTCCTTCCCATTAGATGGCTT 449 AGG American 6959 −1GTTGCCCCCTCCTCTCTCCTTCCCATTAGA 450 TGG American 6974 1GTGACCTAAGCCATCTAATGGGAAGGAGAG 451 AGG American 6977 1ACCTAAGCCATCTAATGGGAAGGAGAGAGG 452 AGG American 6979 1CTAAGCCATCTAATGGGAAGGAGAGAGGAG 453 GGG American 6980 1TAAGCCATCTAATGGGAAGGAGAGAGGAGG 454 GGG American 6991 −1GCCGCAGGTCAATGTCCATTGAGAATCCTA 455 TGG American 7016 −1GCATAGATGGCCCAAGCTGAGGCTGGCCGC 456 AGG American 7039 −1GGGTAATGAAAGTTGTCAAGGCAGCATAGA 457 TGG American 7051 −1GTTGGACGGCTGGGGTAATGAAAGTTGTCA 458 AGG American 7096 −1CCATCGCCATTAAGGAGTAGTTGTTGTATG 459 AGG American 7242 −1TGCGCCACGAGCAAAATGATGGCCACTATT 460 AGG American 7253 −1AGTACATGTAGTGCGCCACGAGCAAAATGA 461 TGG American 7289 1CTCGTGGCGCACTACATGTACTTGATCCCA 462 GGG American 7329 1CAGCAGCTGCGCGTGCTGCCCAGAAGAGAA 463 CGG American 7356 −1ATGTCAGTCACCACTATTCCATCCACAACA 464 GGG American 7428 1TTGACCCCCAAGTGGAGAAAAAGATGGGAC 465 AGG American 7466 −1CCCCCCACCCCCAGGCGGTCCGCGACAGTA 466 TGG American 7484 −1TGATCAGGGCCCCAGCCTCCCCCCACCCCC 467 AGG American 7499 1TCGCGGACCGCCTGGGGGTGGGGGGAGGCT 468 GGG American 7500 1CGCGGACCGCCTGGGGGTGGGGGGAGGCTG 469 GGG American 7508 −1CCCACAAAGTGGAAGTTGCGGCTGTGATCA 470 GGG American 7509 −1TCCCACAAAGTGGAAGTTGCGGCTGTGATC 471 AGG American 7520 −1TCGGAGAGCCTTCCCACAAAGTGGAAGTTG 472 CGG American 7595 1TCTACAGCCACTTCACTGTGTAACATTTTT 473 AGG American 7596 1CTACAGCCACTTCACTGTGTAACATTTTTA 474 GGG American 7653 1TAATCTACACAGTAACAAGAAACGCTGGCT 475 TGG American 7667 1ACAAGAAACGCTGGCTTGGTCAAGAGACGT 476 GGG American 7668 1CAAGAAACGCTGGCTTGGTCAAGAGACGTG 477 GGG American 7689 1AGAGACGTGGGGGTGGAACAGGAGAGACCC 478 TGG American 7691 −1GGTTCAAGCGGGCCTTCCATTTCTCTCCCA 479 GGG American 7692 −1TGGTTCAAGCGGGCCTTCCATTTCTCTCCC 480 AGG American 7704 1GAACAGGAGAGACCCTGGGAGAGAAATGGA 481 AGG American 7712 −1AGAACTCCAGGGCCGACATCTGGTTCAAGC 482 GGG American 7713 −1TAGAACTCCAGGGCCGACATCTGGTTCAAG 483 CGG American 7722 −1TTGTAGGAGTAGAACTCCAGGGCCGACATC 484 TGG American 7748 −1TGCACACCTCGGTGATGCCTGACTTTTTGT 485 AGG American 7767 1TCTACTCCTACAAAAAGTCAGGCATCACCG 486 AGG American 7769 −1GGGCGCGGCGGGCCTCTTCTCTGCACACCT 487 CGG American 7790 −1CCGTTGCCACACCGTCCTTGAGGGCGCGGC 488 GGG American 7791 −1CCCGTTGCCACACCGTCCTTGAGGGCGCGG 489 CGG American 7815 1CCCGCCGCGCCCTCAAGGACGGTGTGGCAA 490 CGG American 7827 −1CTCAGCTTTGCACTTCCTCGGGACACAGCA 491 TGG American 7868 1GGAAGTGCAAAGCTGAGATGGTTGGTGGAG 492 CGG American 7869 1GAAGTGCAAAGCTGAGATGGTTGGTGGAGC 493 GGG American 7992 −1CTTTGCACCAACACGGGTTCTTCATGACCA 494 GGG American 8043 −1ATATGAAAGACGTCCACCCCACTCTTAAGA 495 CGG American 8051 1TATGGGTGGAACATAGTCCGTCTTAAGAGT 496 GGG American 8052 1ATGGGTGGAACATAGTCCGTCTTAAGAGTG 497 GGG American 8144 1TCATCATCTAGTCCTGAAGTGGAAGAAGCA 498 CGG American 8163 −1CTTTTTTCAAGCCAATCCCCCACCATGGAG 499 AGG American 8168 −1CTGGTCTTTTTTCAAGCCAATCCCCCACCA 500 TGG American 8226 −1TCCAGGGTTTCCATCATAGTGCTGGTGTAT 501 GGG American 8253 −1CCTCCCCCATACCTACGCTGCAGTCGCTCC 502 AGG American 8283 1AGCGACTGCAGCGTAGGTATGGGGGAGGAC 503 TGG American 8306 −1AGACCCAGTACATCTCATGTGTAGAGTTGC 504 GGG American 8307 −1GAGACCCAGTACATCTCATGTGTAGAGTTG 505 CGG American 8357 −1GGAGCTGGCTCGTGGTGGACACACTTTTTA 506 TGG American 8382 −1CTAGGCCCGTCCATGCGCCCCAAGAGGAGC 507 TGG American 8390 1AGTGTGTCCACCACGAGCCAGCTCCTCTTG 508 GGG American 8402 1ACGAGCCAGCTCCTCTTGGGGCGCATGGAC 509 GGG American 8430 1ACGGGCCTAGGAGGCCAGTGAAATATGAGG 510 AGG American 8456 1GAGGAGGATGTGAATCTCGGCTCTGGCACG 511 CGG American 8457 1AGGAGGATGTGAATCTCGGCTCTGGCACGC 512 GGG American 8511 −1TCCGCGTGCTCACTGCGGATCCTTTCAATG 513 CGG American 8516 1AACATGAAGATCATTGGTAACCGCATTGAA 514 AGG American 8535 1ACCGCATTGAAAGGATCCGCAGTGAGCACG 515 CGG American 8568 −1TAGCTTCCATGGTAAGCCCATGTCCTATAT 516 GGG American 8598 1ATAGGACATGGGCTTACCATGGAAGCTATG 517 AGG American 8627 −1ACAGGAGCCTGACAACCCCGTTTATTAGAG 518 AGG American 8645 1TCAGCGTCCTCTCTAATAAACGGGGTTGTC 519 AGG American 8670 1TTGTCAGGCTCCTGTCAAAACCCTGGGATG 520 TGG American 8699 −1TTTGCTGACCATACGGTGTGGTGTCGGTCA 521 TGG American 8705 −1AAACTCTTTGCTGACCATACGGTGTGGTGT 522 CGG American 8711 −1CCTTGAAAACTCTTTGCTGACCATACGGTG 523 TGG American 8736 1CCACACCGTATGGTCAGCAAAGAGTTTTCA 524 AGG American 8769 −1ATGCTCATAACCTGACGAGTGCCTTCTTGG 525 GGG American 8897 1ATCAACAAGGTTCGTAGCAATGCAGCATTA 526 GGG American 8898 1TCAACAAGGTTCGTAGCAATGCAGCATTAG 527 GGG American 8997 −1TACACACAACTCTGGCACTCTCCTCTCAGG 528 TGG American 9056 1AACATGATGGGAAAAAGAGAAAAGAAACAA 529 GGG American 9057 1ACATGATGGGAAAAAGAGAAAAGAAACAAG 530 GGG American 9069 1AAAGAGAAAAGAAACAAGGGGAATTTGGAA 531 AGG American 9075 1AAAAGAAACAAGGGGAATTTGGAAAGGCCA 532 AGG American 9077 −1GCCACATATACCAGATGGCGCGGCTGCCCT 533 TGG American 9107 1GGCAGCCGCGCCATCTGGTATATGTGGCTA 534 GGG American 9108 1GCAGCCGCGCCATCTGGTATATGTGGCTAG 535 GGG American 9164 1CTTGGATTCTTGAACGAGGATCACTGGATG 536 GGG American 9198 1GAGAGAACTCAGGAGGTGGTGTTGAAGGGC 537 TGG American 9228 −1CTTCCTCCTGGTATACGACTCATCTCTTCT 538 AGG American 9254 1CTAGAAGAGATGAGTCGTATACCAGGAGGA 539 AGG American 9299 1GACACTGCTGGCTGGGACACCCGCATTAGC 540 AGG American 9353 1CTAATCACCAACCAAATGGAGAAAGGGCAC 541 AGG American 9354 1TAATCACCAACCAAATGGAGAAAGGGCACA 542 GGG American 9362 −1GGTATGTGTACTTGATTATGGCCAATGCCA 543 AGG American 9374 −1CCACTTTGTTTTGGTATGTGTACTTGATTA 544 TGG American 9393 −1GCTGGTCTAAGGACCTTTACCACTTTGTTT 545 TGG American 9467 1GTTATGGACATTATTTCGAGACAAGACCAA 546 AGG American 9587 1CTAGAGATGCAAGACTTGTGGCTGCTGCGG 547 AGG American 9632 1ACTAACTGGTTGCAGAGCAACGGATGGGAT 548 AGG American 9738 1GGTTCTTGAATGATATGGGAAAAGTTAGGA 549 AGG American 9771 1ACACACAAGAGTGGAAACCCTCAACTGGAT 550 GGG American 9825 −1GGAACCACAATGGACCTCCCGTCCTTGAGA 551 TGG American 9833 1CACCACTTCAACAAGCTCCATCTCAAGGAC 552 GGG American 9836 1CACTTCAACAAGCTCCATCTCAAGGACGGG 553 AGG American 9857 −1CCCGGCCAATCAGTTCATCTTGGTGGCGGC 554 AGG American 9881 1CCCTGCCGCCACCAAGATGAACTGATTGGC 555 CGG American 9882 1CCTGCCGCCACCAAGATGAACTGATTGGCC 556 GGG American 9903 1TGATTGGCCGGGCCCGCGTCTCTCCAGGGG 557 CGG American 9921 −1GCATATGATTTTGCTAGGCAAGCAGTCTCC 558 CGG American 9936 −1AGCTGCCACATTTGCGCATATGATTTTGCT 559 AGG American 9969 −1ATCAGTCGGAGGTCCCTTCTGTGGAAATAA 560 AGG American 9980 1CAAATGTGGCAGCTCCTTTATTTCCACAGA 561 AGG American 9981 1AAATGTGGCAGCTCCTTTATTTCCACAGAA 562 GGG American 9993 −1ACAGATGAACAAATGGCATTGGCCATCAGT 563 CGG American 10010 −1GAACCCAGTCAACTGGCACAGATGAACAAA 564 TGG American 10091 −1CTCTGTTCCACACCACAAGCATGTCTTCAG 565 TGG American 10160 −1AATAGGGAATGTCTGTCCATTTCGTAACTG 566 GGG American 10161 −1AAATAGGGAATGTCTGTCCATTTCGTAACT 567 GGG American 10250 −1TGTTGACTGTGTTTTTAATGTTCTCAGCCC 568 AGG American 10326 −1TCTTCACCCAAGTAGCGAACTTGGGTGGAT 569 AGG Asian 469 −1CACTCCCACGTCTAGTGACCTCCACTGCCA 570 TGG Asian 722 −1CTTCTAGATCTCCGTGCTTCACCTTTTTTG 571 TGG Asian 839 −1TTCCTGAATATCCAATTTTCGACTCTAATC 572 AGG Asian 904 −1CTTTTTGGCTCGTTGAACTTCCCAAAAGCC 573 AGG Asian 1075 −1TGTCGACAGCCGGTTTGTCCTGTGCCATTA 574 CGG Asian 1091 1GTTGTGTTACCGTAATGGCACAGGACAAAC 575 CGG Asian 1172 1TAAGATCCTATTGCTATGAGGCATCAATAT 576 CGG Asian 1472 1CAGGACATGAAACTGATGAGAATAGAGCGA 577 AGG Asian 1906 −1CAGCCGGGATCTTGGTGAATGTGAACGCTG 578 CGG Asian 1993 −1TGTCCACCGCCATCTGAGCTGGAACCTTGC 579 AGG Asian 2390 1GGTTCTCACAAATTCTCATTGGAACGTTGC 580 TGG Asian 2537 1ACTTCTCAAAGAAGGAAACGAGATGCGGTA 581 CGG Asian 2644 1GCAGCAGCAGTCAAGCAAGCCTGGGRAGAT 582 GGG Asian 3140 −1TTTGGCCATTCACATGTTTTCATCTCGATC 583 AGG Asian 3712 −1CAAAGGTGGCACCCATCAAAATTGCAAGCT 584 TGG Asian 3872 −1GAGATCGCAGTTTGCAGAAGACACGAAGCC 585 AGG Asian 4102 1TGCGGGGGGTTCATGCTTCTCTCTCTGAAG 586 GGG Asian 4106 1GGGGGTTCATGCTTCTCTCTCTGAAGGGGA 587 AGG Asian 4130 −1GCGGTGAGTCCCAAGGCCATGACAAATGGT 588 AGG Asian 4292 1TATGCGCGTTGGCCGGAGGGTTCGCCAAGG 589 CGG Asian 4454 1CTGGAAACAGTCCCCGGCTCGATGTGGCAC 590 TGG Asian 4754 −1GCGGATCCTTTTGTGACGTGCCACATAGTG 591 TGG Asian 5195 −1ACTCTCCTGGTTTTCCCAGCTCCAGGATGC 592 AGG Asian 5371 1ATGACAACAGCAGTCAATGTCACCCATTCT 593 GGG Asian 5569 −1AGTCCGGGAATGCGTCACGGGTTCCTGGTG 594 GGG Asian 5570 −1GAGTCCGGGAATGCGTCACGGGTTCCTGGT 595 GGG Asian 5594 −1TCGGTGTCCATAATTGGTGAGTTGGAGTCC 596 GGG Asian 6347 1ACACCATAATGGAAGACAGTGTGCCGGCAG 597 AGG Asian 6475 −1GCAATGTTCCCAGGGCTTCCATCACTCCAA 598 AGG Asian 6503 1TTGGAGTGATGGAAGCCCTGGGAACATTGC 599 CGG Asian 6887 1ACCAAATGGCAATCATCATCATGATAGCAG 600 TGG Asian 7082 1CAACTTTCATCACCCCAGCCGTCCAACATG 601 CGG Asian 7206 1AT-GGGACTTTGGAGTCCCGCTGCTAATGA 602 TGG Asian 7571 −1CCCTAAAAATGTTACACAGTGAAGTGGCTG 603 TGG Asian 7677 1CTGGCTTGGTCAAGAGACGTGGGGGTGGAA 604 CGG Asian 7716 −1GAGTAGAACTCTAGGGCCGACATCTGGTTC 605 AGG Asian 8453 −1CTTCAGCGCAGCTTACCACAGCCCGCGTGC 606 CGG Asian 9120 1TCTGGTATATGTGGCTAGGGGCTAGATTCC 607 TGG Asian 9123 −1TCGTTCAAGAATCCAAGGGCTTCGAACTCC 608 AGG Asian 9516 1TCACTTACGCTCTTAATACATTCACCAACC 609 TGG American 650 1GCTATGAATGCCCTATGCTGGATGAGGGGG 610 TGG American 1507 −1CTAGGCTTCCAAACCCCCCCAGGGTGGCTT 611 CGG American 1519 1AATTCACCAAGAGCCGAAGCCACCCTGGGG 612 GGG American 2068 −1TCTTAGAGTTCTCAGTGCTTTCAGTGATTA 613 CGG American 2174 −1TTTCCAATGGTGCTGCCACTCCTGTGCCAG 614 TGG American 2608 −1AGGCTTGCTTGACTGCTGCTGCCAATCTAC 615 GGG American 2609 −1CAGGCTTGCTTGACTGCTGCTGCCAATCTA 616 CGG American 2612 1ACAAGTACCATCCTGACTCCCCCCGTAGAT 617 TGG American 3277 −1GCTCTTCACTGTGCCATGGCCCTTTCATTT 618 GGG American 3278 −1AGCTCTTCACTGTGCCATGGCCCTTTCATT 619 TGG American 3569 −1AGCAGAATCACAAGCACTCCAAGGGAGAAG 620 TGG American 3877 −1AGGCGGAGATCGCAGTTTGCAAAAGACACG 621 AGG American 4007 1CACGCACTGATAACATCACCTTGGCAATCC 622 TGG American 4094 −1TTCTTCACACTGCCTTTTCCCTTCAGAGAG 623 AGG American 4148 −1GGGTCGACCAGCCTCACAGCGGTTAGTCCC 624 AGG American 4262 −1TTGGCGAACCCTCCAGCCAATGCGCATATC 625 AGG American 4478 1TGGCGCTAGATGAGAGTGGTGATTTCTCCC 626 TGG American 4520 1ACGGTCCCCCCATGAGAGAGATCATACTCA 627 AGG American 4985 1TATTTAAGACAAAGGATGGGGACATTGGAG 628 CGG American 5312 1CAACCAGGGTTGTCGCTGCTGAAATGGAGG 629 AGG American 6095 −1ATGAGGCCATCTTGGAGGTAAATATTGTCA 630 AGG American 6166 −1GCTCCGTCCTAAGCTTGAACTCTCCCTCAA 631 TGG American 6440 1GTTCAGATCATGCGGCCCTGAAGTCATTCA 632 AGG American 6620 −1CCCAGCAACCCCAAAAGCATAATGGTCTCT 633 AGG American 6878 1CCCAGGACAACCAAATGGCAATCATCATCA 634 TGG American 7039 −1GGGTAATGAAAGTTGTCAAGGCAGCATAGA 635 TGG American 7051 −1GTTGGACGGCTGGGGTAATGAAAGTTGTCA 636 AGG American 7096 −1CCATCGCCATTAAGGAGTAGTTGTTGTATG 637 AGG American 7408 −1TAGCACCTGTCCCATCTTTTTCTCCACTTG 638 GGG American 7409 −1GTAGCACCTGTCCCATCTTTTTCTCCACTT 639 GGG American 7520 −1TCGGAGAGCCTTCCCACAAAGTGGAAGTTG 640 CGG American 7731 1GGAAGGCCCGCTTGAACCAGATGTCGGCCC 641 TGG American 7815 1CCCGCCGCGCCCTCAAGGACGGTGTGGCAA 642 CGG American 7868 1GGAAGTGCAAAGCTGAGATGGTTGGTGGAG 643 CGG American 7869 1GAAGTGCAAAGCTGAGATGGTTGGTGGAGC 644 GGG American 8609 −1CGTTTATTAGAGAGGACGCTGACCCTTGTG 645 TGG American 9015 −1CTTTTTCCCATCATGTTGTACACACAACTC 646 TGG American 9881 1CCCTGCCGCCACCAAGATGAACTGATTGGC 647 CGG American 9882 1CCTGCCGCCACCAAGATGAACTGATTGGCC 648 GGG American 10278 1GGGCTGAGAACATTAAAAACACAGTCAACA 649 TGG

TABLE 6 Sequences of Toehold Switch Sensors and Corresponding Target Sequences inZika Genome. Target Target RNA Fragment Used for sequenceInitial Sensor Screening in Zika Location A Series SensorsB Series Sensors Genome Genome Genome virus in Sensor Sensor SensorSensor Start End fragment genome genome Name sequence Name sequenceSequence site site length UUGAGAG 3027 1A UCUUCAGCC 25B UCUUCAGCCGGGCAGUGAUCU 3007 3170 164 UGAGAAG UCCAUGUGU UCCAUGUGU AGGCUACUGGAUAAUGACA CAUUCUUCU CAUUCUUCU UGAGAGUGAGAA CAUGGAG CACUCUCAAG CACUCUCAAGAAUGACACAUG GCUGAAG UUAUAGUUA GGACUUUAG GAGGCUGAAGAG A (SEQ IDUGAACAGAG AACAGAGGA GGCCCAUCUGAU NO: 650) GAGACAUAAC GAUAAAGAUCGAGAUGAAAAC AUGAACUUG GUUGAGAGU AUGUGAAUGGCC AGAAACCAAG GAGUAACCUAAAGUCCCACAC UUAACCUGG GGCGGCAGC AUUGUGGACAGA CGGCAGCGCA GCAAAAGUGGAAUAGAAGA AAAG (SEQ ID (SEQ ID NO: GAGUGAUCUGAU NO: 674) 698)CAUACCCAAGUC UUUAGCUGGGC (SEQ ID NO: 722) AUGAUGG 8963 2A AAAUUCCCCU 26BAAAUUCCCC GGGUGCCAGAGU 8941 9098 158 GAAAAAG UGUUUCUUU UUGUUUCUU UGUGUGUACAAC AGAAAAG UCUCUUUUU UUCUCUUUU AUGAUGGGAAAA AAACAAG CCCAUCAUGUUCCCAUCAU AGAGAAAAGAAA GGGAAUU UAUAGUUAU GGACUUUAG CAAGGGGAAUUUU (SEQ ID GAACAGAGG AACAGAGGA GGAAAGGCCAAG NO: 651) AGACAUAACA GAUAAAGAUGGCAGCCGCGCC UGAACAUGA GAUGAUGGG AUCUGGUAUAUG UGAACCAUG AAAAAACCUUGGCUAGGGGCU UUAACCUGG GGCGGCAGC AGAUUUCUAGAG CGGCAGCGCA GCAAAAGUUCGAAGCCCUU AAAG (SEQ ID (SEQ ID NO: GGAUUCUUGAAC NO: 675) 699)GAGGAUCACUGG AUGG (SEQ ID NO: 723) GACACAG 1373 3A UUUCGCUCU 27BUUUCGCUCU GGGCCAGCACAG 1348 1494 147 GACAUGA AUUCUCAUCA AUUCUCAUCUGGGAUGAUCGU AACUGAU GUUUCAUGU AGUUUCAUG  UAAUGACACAGG GAGAAUA CCUGUGUCGUCCUGUGUC ACAUGAAACUGA GAGCGAA UUAUAGUUA GGACUUUAG UGAGAAUAGAGCA (SEQ ID UGAACAGAG AACAGAGGA GAAAGUUGAGAU NO: 652) GAGACAUAAC GAUAAAGAUAACGCCCAAUUC AUGAACGACA GGACACAGG ACCAAGAGCCGA CAAACGUCGU ACACAACCUAGCCACCCUGGG UAACCUGGC GGCGGCAGC GGGGUUUGGAAG GGCAGCGCAA GCAAAAGCCUAGGACUUGA AAG (SEQ ID (SEQ ID NO: UUGUGAACCGAG NO: 676) 700)GACAGG (SEQ ID NO: 724) UGGAAAA 2610 4A GCUCCCCUUC 28B GCUCCCCUUGGGCGGGAUCUC 2586 2733 148 CAUCAUG UACUGAUCU CUACUGAUC CUCUGUUUCAAGUGGAGAU CCACAUGAUG UCCACAUGA AAUGGAAAACAU CAGUAGA UUUUCCAGU UGUUUUCCACAUGUGGAGAUC AGGGGAG UAUAGUUAU GGACUUUAG AGUAGAAGGGGA C (SEQ IDGAACAGAGG AACAGAGGA GCUCAACGCAAU NO: 653) AGACAUAACA GAUAAAGAUCCUGGAAGAGAA UGAACUGGA GUGGAAAAC UGGAGUUCAACU AAAACCCAGU AUCAAACCUGACGGUCGUUGU UAACCUGGC GGCGGCAGC GGGAUCUGUAAA GGCAGCGCAA GCAAAAGAAACCCCAUGUG AAG (SEQ ID (SEQ ID NO: GAGAGGUCCACA NO: 677) 701)GAGAUU (SEQ ID NO: 725) GGGGAAA 256 5A AUUAUUUCC 29B AACUUCUUUGGGCCAUCACUG 220 385 166 AAAGAGG AUAGCCUCU AACUUCUUU GGUCUCAUCAAUCUAUGGA UUUUUCCCC AUUAUUUCC AGAUGGGGUUCA AAUAAUA GUUAUAGUU AUAGCCUCUGUGGGGAAAAAA AAGAAGU AUGAACAGA UUUUUCCCC GAGGCUAUGGAA U (SEQ IDGGAGACAUA GGACUUUAG AUAAUAAAGAAG NO: 654) ACAUGAACG AACAGAGGAUUCAAGAAAGAU GGGAAAACCC GAUAAAGAU CUGGCUGCCAUG CGUUAACCU GGGGGAAAACUGAGAAUAAUC GGCGGCAGC AAGAAACCU AAUGCUAGGAAG GCAAAAG GGCGGCAGCGAGAAGAAGAGA (SEQ ID NO: GCAAAAG CGAGGCGCAGAU 678) (SEQ ID NO:ACUAGUGUCGGA 702) AUUGUUGGCCUC (SEQ ID NO: 726) GAUAACG 1414 6AAGGGUGGCU 30B AGGGUGGCU GGGAAUGCUGUC 1327 1494 168 CCCAAUU UCGGCUCUUUCGGCUCUU AGUUCAUGGCUC CACCAAG GGUGAAUUG GGUGAAUUG CCAGCACAGUGG AGCCGAAGGCGUUAUC GGCGUUAUC GAUGAUCGUUAA GCCACCC GUUAUAGUU GGACUUUAGUGACACAGGACA U (SEQ ID AUGAACAGA AACAGAGGA UGAAACUGAUGA NO: 655)GGAGACAUA GAUAAAGAU GAAUAGAGCGAA ACAUGAACGA GGAUAACGC AGUUGAGAUAACUAACAACAUC CCAUAACCU GCCCAAUUCACC GUUAACCUG GGCGGCAGC AAGAGCCGAAGCGCGGCAGCG GCAAAAG CACCCUGGGGGG CAAAAG (SEQ (SEQ ID NO:  GUUUGGAAGCCUID NO: 679) 703) AGGACUUGAUUG UGAACCGAGGAC AGG (SEQ ID NO: 727) UUGAAGA8841 7A CUUCCACUGC 31B CUUCCACUG GGGAGAAGGAUG 8729 8920 192 GGAAAAAAGUCUUCCAC CAGUCUUCC GUCUCUUCCUGG GAGUGGA UCUUUUUCC ACUCUUUUUUUGUGGAAAGAG AGACUGC UCUUCAAGU CCUCUUCAA CUAGGCAAACAC AGUGGAA UAUAGUUAUGGACUUUAG AAACGGCCACGA G (SEQ ID GAACAGAGG AACAGAGGA GUCUGUACCAAANO: 656) AGACAUAACA GAUAAAGAU GAAGAGUUCAUC UGAACUUGA GUUGAAGAGAACAAGGUUCGU AGAACCAAGU GAAAAACCU AGCAAUGCAGCA UAACCUGGC GGCGGCAGCUUAGGGGCAAUA GGCAGCGCAA GCAAAAG UUUGAAGAGGAA AAG (SEQ ID (SEQ ID NO: AAAGAGUGGAAG NO: 680) 704) ACUGCAGUGGAA GCUGUGAACGAU CCAAGGUUCUGGGCUCUAGUGGAC AAGGAAAGA (SEQ ID NO: 728) UUUUGC 7188 8A CUGGGAUCA 32BCUGGGAUCA GGGCUGACCCUA 7166 7299 134 UCGUGGC AGUACAUGU AGUACAUGUAUAGUGGCCAUC GCACUAC AGUGCGCCAC AGUGCGCCA AUUUUGCUCGUG AUGUACU GAGCAAAAGCGAGCAAAA GCGCACUACAUG UGAUCCC UUAUAGUUA GGACUUUAG UACUUGAUCCCA AG (SEQUGAACAGAG AACAGAGGA GGGCUGCAGGCA ID NO: GAGACAUAAC GAUAAAGAUGCAGCUGCGCGU 657) AUGAACUUU GUUUUGCUC GCUGCCCAGAAG UGCAACAAAG GUGUAACCUAGAACGGCAGCU UUAACCUGG GGCGGCAGC GGCAUCAUGAAG CGGCAGCGCA GCAAAAGAACCCUGUUGUG AAAG (SEQ ID (SEQ ID NO: GAUGG (SEQ ID NO: 681) 705)NO: 729) UUGCUAC 7144 9A GUCAGGGGU 33B ACUAUUAGG GGGUUUGGUAU 7078 7228151 UCACAAU GUUAAUUGU ACUAUUAGG GGGCAAAGGGAU UAACACC GAGUAGCAA GUCAGGGGUGCCAUUCUACGC CCUGACC GUUAUAGUU GUUAAUUGU AUGGGACUUUGG CUAAUAG AUGAACAGAGAGUAGCAA AGUCCCGCUGCU U (SEQ ID GGAGACAUA GGACUUUAG AAUGAUAGGUUGNO: 658) ACAUGAACU AACAGAGGA CUACUCACAAUU UGCUAAACCA GAUAAAGAUAACACCCCUGAC AGUUAACCU GUUGCUACU CCUAAUAGUGGC GGCGGCAGC CACUAACCUCAUCAUUUUGCU GCAAAAG GGCGGCAGC CGUGGCGCACUA (SEQ ID NO: GCAAAAGCAUGUACUUGAU 682) (SEQ ID NO: CCCAGGGCUG 706) (SEQ ID NO: 730) ACCACCU7022 10A AAGGAGUAG 34B CAUCGCCAUU GGGCCAUCUAUG 6966 7141 176 CAUACAAUUGUUGUAU CAUCGCCAU CUGCCUUGACAA CAACUAC GAGGUGGUG UAAGGAGUACUUUCAUUACCC UCCUUAA UUAUAGUUA GUUGUUGUA CAGCCGUCCAAC UGGCGAU UGAACAGAGUGAGGUGGU AUGCAGUGACCA G (SEQ ID GAGACAUAAC GGACUUUAG CCUCAUACAACANO: 659) AUGAACACCA AACAGAGGA ACUACUCCUUAA CCAACGGUG GAUAAAGAUUGGCGAUGGCCA UUAACCUGG GACCACCUCA CGCAAGCUGGAG CGGCAGCGCA UAUAACCUGUGUUGUUUGGU AAAG (SEQ ID GCGGCAGCG AUGGGCAAAGGG ID NO: 707) CAAAAG (SEQAUGCCAUUCUAC NO: 683) GCAUGGGACUUU GGAGUCCCGCUG CUAAUGAUA(SEQ ID NO: 731) ACCACAA 3563 11A CACUGCCAUU 35B CACUGCCAU GGGAGAAGGGUG3521 3702 182 AGAUCAU GAUGUGCUU UGAUGUGCU AUUCUGCUCAUG CAUAAGC AUGAUGAUCUAUGAUGAU GUGCAGGAAGGG ACAUCAA UUUGUGGUG CUUUGUGGU UUGAAGAAGAGA UGGCAGUUUAUAGUUA GGACUUUAG AUGACCACAAAG G (SEQ ID UGAACAGAG AACAGAGGAAUCAUCAUAAGC NO: 660) GAGACAUAAC GAUAAAGAU ACAUCAAUGGCA AUGAACACCAGACCACAAA GUGCUGGUAGCU CAAACGGUG GAUAAACCU AUGAUCCUGGGA UUAACCUGGGGCGGCAGC GGAUUUUCAAUG CGGCAGCGCA GCAAAAG AGUGACCUGGCU AAAG (SEQ ID(SEQ ID NO:  AAGCUUGCAAUU NO: 684) 708) UUGAUGGGUGCC ACCUUCGCGGAAAUGAACACUGGA GGAGAUGUAGC (SEQ ID NO: 732) AGACAGA 5721 12A CCCACUCUUG36B CCCACUCUU GGGAGAAGGGUU 5628 5850 223 GUUCCAG AUGUUUUGU GAUGUUUUGUGUUCCAAGCGU AAAACAA UUUCUGGAA UUUUCUGGA GAGGAACGGCAA AACAUCA CUCUGUCUGACUCUGUCU UGAGAUCGCAGC AGAGUGG UUAUAGUUA GGACUUUAG UUGUCUGACAAAG (SEQ ID UGAACAGAG AACAGAGGA GGCUGGAAAACG NO: 661) GAGACAUAAC GAUAAAGAUGGUCAUACAGCU AUGAACAGAC GAGACAGAG CAGCAGAAAGAC AGAACUCUG UUCCAACCUUUUUGAGACAGA UUAACCUGG GGCGGCAGC GUUCCAGAAAAC CGGCAGCGCA GCAAAAGAAAACAUCAAGA AAAG (SEQ ID (SEQ ID NO: GUGGGACUUUGU NO: 685) 709)CGUGACAACUGA CAUUUCAGAGAU GGGCGCCAACUU UAAAGCUGACCG UGUCAUAGAUUCCAGGAGAUGCCU AAAGCCGGUCAU ACU (SEQ ID NO: 733) UGCACAA 3368 13AAUCUUUAGC 37B AUCUUUAGC GGGAGAUCAACC 3316 3445 130 UGCCCCC CCGGAACGACCCGGAACGA ACUGCAAGCGGA ACUGUCG AGUGGGGGC CAGUGGGGG AGGGUGAUCGAG UUCCGGGAUUGUGCAG CAUUGUGCA GAAUGGUGCUGC CUAAAGA UUAUAGUUA GGACUUUAGAGGGAGUGCACA U (SEQ ID UGAACAGAG AACAGAGGA AUGCCCCCACUG NO: 662)GAGACAUAAC GAUAAAGAU UCGUUCCGGGCU AUGAACUGC GUGCACAAU AAAGAUGGCUGUACAAACGCAG GCCGAACCU UGGUAUGGAAUG UUAACCUGG GGCGGCAGC GAGAUAAGGCCCCGGCAGCGCA GCAAAAG AGGAAAGAACCA AAAG (SEQ ID (SEQ ID NO:(SEQ ID NO: 734) NO: 686) 710) GACACCG 1598 14A UGCUUCUUU 38B UGCUUCUUUGGGAGUGGUUCC 1555 1711 157 GAACUCC GUUGUUCCA GUUGUUCCA ACGACAUUCCAUACACUGG GUGUGGAGU GUGUGGAGU UACCUUGGCACG AACAACA UCCGGUGUC UCCGGUGUCCUGGGGCAGACA AAGAAGC GUUAUAGUU GGACUUUAG CCGGAACUCCAC A (SEQ IDAUGAACAGA AACAGAGGA ACUGGAACAACA NO: 663) GGAGACAUA GAUAAAGAUAAGAAGCACUGG ACAUGAACGA GGACACCGG UAGAGUUCAAGG CACCAACGUC AACAAACCUACGCACAUGCCA GUUAACCUG GGCGGCAGC AAAGGCAAACUG GCGGCAGCG GCAAAAGUCGUGGUUCUAG CAAAAG (SEQ (SEQ ID NO: GGAGUCAAGAAG ID NO: 687) 711)GAGCAGUUCACA CG (SEQ ID NO: 735) GUUUGCC 6379 15A ACUCCAAAAG 39BACUCCAAAA GGGUGGACGCCA 6330 6458 129 GCUGGGA CCGCUCCUCU GCCGCUCCUGAGUUUGUUCAG AAAGAGG UUUCCCAGC CUUUUCCCA AUCAUGCGGCCC AGCGGCU GGCAAACGUGCGGCAAAC UGAAGUCAUUCA UUUGGA UAUAGUUAU GGACUUUAG AGGAGUUUGCCG GU (SEQGAACAGAGG AACAGAGGA CUGGGAAAAGAG ID NO: AGACAUAACA GAUAAAGAUGAGCGGCUUUUG 664) UGAACGUUU GGUUUGCCG GAGUGAUGGAAG GCAACAACGU CUGCAACCUCCCUGGGAACAC UAACCUGGC GGCGGCAGC UGCCAGGACACA GGCAGCGCAA GCAAAAGUGACAGAGAGAU AAG (SEQ ID (SEQ ID NO: (SEQ ID NO: 736) NO: 688) 712)GGCAGAA 6277 16A ACUCUUUUC 40B ACUCUUUUC GGGCUGCCGGAA 6198 6351 154GUGUGG UCUCCGUGU UCUCCGUGU UAACCUACACAG ACCAGAC CUGGUCCACA CUGGUCCACAUAGAAGAUGGU ACGGAGA CUUCUGCCG ACUUCUGCC GCUUUGAUGGCA GAAAAGA UUAUAGUUAGGACUUUAG CGACCAACAACA GU (SEQ UGAACAGAG AACAGAGGA CCAUAAUGGAAG ID NO:GAGACAUAAC GAUAAAGAU ACAGUGUGCCGG 665) AUGAACGGC GGGCAGAAG CAGAAGUGUGGAAGAAACGCCG UGUAAACCU CCAGACACGGAG UUAACCUGG GGCGGCAGC AGAAAAGAGUGCCGGCAGCGCA GCAAAAG UCAAACCGAGGU AAAG (SEQ ID (SEQ ID NO: GGAUGGACGCCANO: 689) 713) GAGUUUGUUCAG A (SEQ ID NO: 737) CUGAUCG 3071 17A GGACUUUGG41B GGACUUUGG GGGCUACUGGAU 3017 3170 154 AGAUGAA CCAUUCACAU CCAUUCACAUGAGAGUGAGAA   AACAUGU GUUUUCAUC UGUUUUCAU GAAUGACACAUG GAAUGGCUCGAUCAGG CUCGAUCAG GAGGCUGAAGAG CAAAGUC UUAUAGUUA GGACUUUAGGGCCCAUCUGAU C (SEQ ID UGAACAGAG AACAGAGGA CGAGAUGAAAAC NO: 666)GAGACAUAAC GAUAAAGAU AUGUGAAUGGCC AUGAACCUG GCUGAUCGA AAAGUCCCACACAUCAACCAGG GAUGAACCU AUUGUGGACAGA UUAACCUGG GGCGGCAGC UGGAAUAGAAGACGGCAGCGCA GCAAAAG GAGUGAUCUGAU AAAG (SEQ ID (SEQ ID NO: CAUACCCAAGUCNO: 690) 714) UUUAGCUGGGC (SEQ ID NO: 738) GAGCCAG 6761 18A UUGGUUGUC42B UUGGUUGUC GGGCAGCCAGAA 6702 6874 173 AAAAGCA CUGGGGAGA CUGGGGAGAUUGCAUGUGUCC AAGAUCU UCUUUGCUU UCUUUGCUU UCAUUGUUGUGU CCCCAGG UUCUGGCUCUUCUGGCUC UCCUAUUGCUGG ACAACCA GUUAUAGUU GGACUUUAG UGGUGCUCAUACA (SEQ ID AUGAACAGA AACAGAGGA CUGAGCCAGAAA NO: 667) GGAGACAUA GAUAAAGAUAGCAAAGAUCUC ACAUGAACGA GGAGCCAGA CCCAGGACAACC GCCAAACCUC AAAGAACCUAAAUGGCAAUCA GUUAACCUG GGCGGCAGC UCAUCAUGGUAG GCGGCAGCG GCAAAAGCAGUAGGUCUUC CAAAAG (SEQ (SEQ ID NO:  UGGGCUUGAUUA ID NO: 691) 715)CCGCCAAUGAAC UCGGAUGGUUGG AGAGAACA (SEQ ID NO: 739) CUUAACA 9431 19AAAUGAGUUG 43B AAUGAGUUG GGGAGCGGACAA 9404 9581 178 CAUUUAC CACCACUAGGCACCACUAG GUUGUCACUUAC CAACCUA UUGGUAAAU GUUGGUAAA GCUCUUAACACA GUGGUGGUGUUAAGG UGUGUUAAG UUUACCAACCUA CAACUCA UUAUAGUUA GGACUUUAGGUGGUGCAACUC UU (SEQ UGAACAGAG AACAGAGGA AUUCGGAAUAUG ID NO: GAGACAUAACGAUAAAGAU GAGGCUGAGGAA 668) AUGAACCUU GCUUAACAC  GUUCUAGAGAUG AACAACAAGGAUUGAACCU CAAGACUUGUGG UUAACCUGG GGCGGCAGC CUGCUGCGGAGG CGGCAGCGCAGCAAAAG UCAGAGAAAGUG AAAG (SEQ ID (SEQ ID NO:  ACUAACUGGUUG NO: 692)CAGAGCAACGGA 716) UGGGAUAGGCUC AAACGAAUGG (SEQ ID NO: 740) GCGGUAC 246620A CUUCAACGUC 44B CUUCAACGU GGGUGCUCGGUG 2429 2578 150 AGGGGU GUUAUAGACCGUUAUAGA GACUUCUCAAAG GUUCGUC GAACACCCCU CGAACACCCC AAGGAGACGAGAUAUAACG GUACCGCG U UGUACCGCG UGCGGUACAGGG ACGUUGA UAUAGUUAU GACUUUAGAGUGUUCGUCUAU AG (SEQ GAACAGAGG ACAGAGGAG AACGACGUUGAA ID NO: AGACAUAACAAUAAAGAUG GCCUGGAGGGAC 669) UGAACGCGG GCGGUACAG AGGUACAAGUAC UAAACCGCGUGGAAACCUG CAUCCUGACUCC UAACCUGGC GCGGCAGCG CCCCGUAGAUUG GGCAGCGCAACAAAAG (SEQ GCAGCAGCAGUC AAG (SEQ ID ID NO: 717) AAGCAAGCCUGG NO: 693)GAAGAU (SEQ ID NO: 741) GAGGCUG 9476 21A CCACAAGUCU 45B CCACAAGUCGGGAGUGGUGCA 9451 9584 134 AGGAAGU UGCAUCUCU UUGCAUCUC ACUCAUUCGGAAUCUAGAG AGAACUUCCU UAGAACUUC UAUGGAGGCUGA AUGCAAG CAGCCUCGU CUCAGCCUCGGAAGUUCUAGA ACUUGUG UAUAGUUAU GGACUUUAG GAUGCAAGACUU G (SEQ IDGAACAGAGG AACAGAGGA GUGGCUGCUGCG NO: 670) AGACAUAACA GAUAAAGAUGAGGUCAGAGAA UGAACGAGG GGAGGCUGA AGUGACUAACUG CUAACCUCGU GGACAACCUGUUGCAGAGCAA UAACCUGGC GGCGGCAGC CGGAUGGGAUAG GGCAGCGCAA GCAAAAGGCUCAAACGAAU AAG (SEQ ID (SEQ ID NO: GGCAG (SEQ ID NO: 694) 718)NO: 742) GGCACAG 3225 22A AUUCCUCAAA 46B AUUCCUCAA GGGCAAUACCAG 31843334 151 UGAAGAG CCGAAUUUCA ACCGAAUUU AGAGGGCUACAG CUUGAAA AGCUCUUCACCAAGCUCUU GACCCAAAUGAA UUCGGU UGUGCCGUU CACUGUGCC AGGGCCAUGGCA UUGAGGAAUAGUUAUG GGACUUUAG CAGUGAAGAGCU AU (SEQ AACAGAGGA AACAGAGGAUGAAAUUCGGUU ID NO: GACAUAACAU GAUAAAGAU UGAGGAAUGCCC 671) GAACGGCACAGGGCACAGU AGGCACUAAGGU AACGCCGUUA GAAAAACCU CCACGUGGAGGA ACCUGGCGGGGCGGCAGC AACAUGUGGAAC CAGCGCAAAA GCAAAAG GAGAGGACCAUC G (SEQ ID NO:(SEQ ID NO: UCUGAGAUCAAC 695) 719) CACUGCAAGC (SEQ ID NO: 743) CAUCUAA6890 23A UAUGGUUGC 47B UAUGGUUGC GGGAGUAGGUCU 6820 6952 133 UGGGAAGCCCCUCCUCU CCCCUCCUCU UCUGGGCUUGAU GAGAGAG CUCCUUCCCA CUCCUUCCCUACCGCCAAUGA GAGGGG UUAGAUGGU AUUAGAUGG ACUCGGAUGGUU GCAACCA UAUAGUUAUGACUUUAGA GGAGAGAACAAA UA (SEQ GAACAGAGG ACAGAGGAG GAGUGACCUAAG ID NO:AGACAUAACA AUAAAGAUG CCAUCUAAUGGG 672) UGAACCAUCU CAUCUAAUG AAGGAGAGAGGAAAACAUGGU GGAAACCUG GGGGGCAACCAU UAACCUGGC GCGGCAGCG AGGAUUCUCAAUGGCAGCGCAA CAAAAG (SEQ GGACAUUGACCU AAG (SEQ ID ID NO: 720) GCGG (SEQ IDNO: 696) NO: 744) GAUAGGU 9620 24A AUCAUUCAA 48B AUCAUUCAA GGGAUAGGCUCA9561 9688 128 UUGCACA GAACCUGAG GAACCUGAG AACGAAUGGCAG UGCCCUC GGCAUGUGCGGCAUGUGC UCAGUGGAGAUG AGGUUCU AAACCUAUCG AAACCUAUC AUUGCGUUGUGA UGAAUGAUUAUAGUUA GGACUUUAG AGCCAAUUGAUG U (SEQ ID UGAACAGAG AACAGAGGAAUAGGUUUGCAC NO: 673) GAGACAUAAC GAUAAAGAU AUGCCCUCAGGU AUGAACGAUGGAUAGGUU UCUUGAAUGAUA AGGAACAUC UGCUAACCU UGGGAAAAGUUA GUUAACCUGGGCGGCAGC GGAAGGACACAC GCGGCAGCG GCAAAAG AAGAGUGG (SEQ CAAAAG (SEQ(SEQ ID NO: ID NO: 745) ID NO: 697) 721) NOTES: 1. The sequence GGG wasadded to the 5′ end of all sensor RNA and RNA fragment sequences forefficient expression by T7 RNA polymerase. If the RNA target sequencebegan with G or GG, only GG or G, respectively, was added to the 5′ endof the sequence. prefix is not shown in the sensor sequences in thetable so that the target 2. The GGG RNA be readily identified. 3. Thecoding sequence of the reporter protein lacZ binding site can was afterthe switch RNA sequences in the tables. 4. Two Zika virus strains addedimmediately AY632535) (KU312312, have sufficient sequence homology to bedetected using the same switch sensors toehold (27B, 32B). 5. TargetRNAs fragments for sensors 7A/3 1B and 11A/35B have a GGGAGAAGG sequenceadded at the 5′ end. 6. Target RNA fragments for sensors 12A/36B have aGGGAGAAG sequence added at the 5′ end.

TABLE 7  Zika virusACAGGUUUUAUUUUGGAUUUGGAAACGAGAGUUUCUGGUCAUGAAAAACCCAA from theAAAAGAAAUCCGGAGGAUUCCGGAUUGUCAAUAUGCUAAAACGCGGAGUAGCC AmericasCGUGUGAGCCCCUUUGGGGGCUUGAAGAGGCUGCCAGCCGGACUUCUGCUGGG genomeUCAUGGGCCCAUCAGGAUGGUCUUGGCGAUUCUAGCCUUUUUGAGAUUCACGG sequenceCAAUCAAGCCAUCACUGGGUCUCAUCAAUAGAUGGGGUUCAGUGGGGAAAAAA (AccessionGAGGCUAUGGAAAUAAUAAAGAAGUUCAAGAAAGAUCUGGCUGCCAUGCUGA number:GAAUAAUCAAUGCUAGGAAGGAGAAGAAGAGACGAGGCGCAGAUACUAGUGU KU312312;CGGAAUUGUUGGCCUCCUGCUGACCACAGCUAUGGCAGCGGAGGUCACUAGAC 10,374-nts)GUGGGAGUGCAUACUAUAUGUACUUGGACAGAAACGAUGCUGGGGAGGCCAUAUCUUUUCCAACCACAUUGGGGAUGAAUAAGUGUUAUAUACAGAUCAUGGAUCUUGGACACACGUGUGAUGCCACCAUGAGCUAUGAAUGCCCUAUGCUGGAUGAGGGGGUGGAACCAGAUGACGUCGAUUGUUGGUGCAACACGACGUCAACUUGGGUUGUGUACGGAACCUGCCAUCACAAAAAAGGUGAAGCACGGAGAUCUAGAAGAGCUGUGACGCUCCCCUCCCAUUCCACUAGGAAGCUGCAAACGCGGUCGCAAACCUGGUUGGAAUCAAGAGAAUACACAAAGCACUUGAUUAGAGUCGAAAAUUGGAUAUUCAGGAACCCUGGCUUCGCGUUAGCAGCAGCUGCCAUCGCUUGGCUUUUGGGAAGCUCAACGAGCCAAAAAGUCAUAUACUUGGUCAUGAUACUGCUGAUUGCCCCGGCAUACAGCAUCAGGUGCAUAGGAGUCAGCAAUAGGGACUUUGUGGAAGGUAUGUCAGGUGGGACUUGGGUUGAUGUUGUCUUGGAACAUGGAGGUUGUGUCACUGUAAUGGCACAGGACAAACCGACUGUCGACAUAGAGCUGGUUACAACAACAGUCAGCAACAUGGCGGAGGUAAGAUCCUACUGCUAUGAGGCAUCAAUAUCAGACAUGGCUUCGGACAGCCGCUGCCCAACACAAGGUGAAGCCUACCUUGACAAGCAAUCAGACACUCAAUAUGUCUGCAAAAGAACGUUAGUGGACAGAGGCUGGGGAAAUGGAUGUGGACUUUUUGGCAAAGGGAGCCUGGUGACAUGCGCUAAGUUUGCAUGCUCCAAGAAAAUGACCGGGAAGAGCAUCCAGCCAGAGAAUCUGGAGUACCGGAUAAUGCUGUCAGUUCAUGGCUCCCAGCACAGUGGGAUGAUCGUUAAUGACACAGGACAUGAAACUGAUGAGAAUAGAGCGAAAGUUGAGAUAACGCCCAAUUCACCAAGAGCCGAAGCCACCCUGGGGGGGUUUGGAAGCCUAGGACUUGAUUGUGAACCGAGGACAGGCCUUGACUUUUCAGAUUUGUAUUACUUGACUAUGAAUAACAAGCACUGGCUGGUUCACAAGGAGUGGUUCCACGACAUUCCAUUACCUUGGCACGCUGGGGCAGACACCGGAACUCCACACUGGAACAACAAAGAAGCACUGGUAGAGUUCAAGGACGCACAUGCCAAAAGGCAAACUGUCGUGGUUCUAGGGAGUCAAGAAGGAGCAGUUCACACGGCCCUUGCUGGAGCUCUGGAGGCUGAGAUGGAUGGUGCAAAGGGAAGGCUGUCCUCUGGCCACUUGAAAUGUCGCCUGAAAAUGGAUAAACUUAGAUUGAAGGGCGUGUCAUACUCCUUGUGUACUGCAGCGUUCACAUUCACCAAGAUCCCGGCUGAAACACUGCACGGGACAGUCACAGUGGAGGUACAGUACGCAGGGACAGAUGGACCUUGCAAGGUUCCAGCUCAGAUGGCGGUGGACAUGCAAACUCUGACCCCAGUUGGGAGGUUGAUAACCGCUAACCCCGUAAUCACUGAAAGCACUGAGAACUCUAAGAUGAUGCUGGAACUUGAUCCACCAUUUGGGGACUCUUACAUUGUCAUAGGAGUCGGGGAGAAGAAGAUCACCCACCACUGGCACAGGAGUGGCAGCACCAUUGGAAAAGCAUUUGAAGCCACUGUGAGAGGUGCCAAGAGAAUGGCAGUCUUGGGAGACACAGCCUGGGACUUUGGAUCAGUUGGAGGCGCUCUCAACUCAUUGGGCAAGGGCAUCCAUCAAAUCUUUGGAGCAGCUUUCAAAUCAUUGUUUGGAGGAAUGUCCUGGUUCUCACAAAUUCUCAUUGGAACGUUGCUGAUGUGGUUGGGUCUGAACGCAAAGAAUGGAUCUAUUUCCCUUAUGUGCUUGGCCUUAGGGGGAGUGUUGAUCUUCUUAUCCACAGCCGUCUCUGCUGAUGUGGGGUGCUCGGUGGACUUCUCAAAGAAGGAGACGAGAUGCGGUACAGGGGUGUUCGUCUAUAACGACGUUGAAGCCUGGAGGGACAGGUACAAGUACCAUCCUGACUCCCCCCGUAGAUUGGCAGCAGCAGUCAAGCAAGCCUGGGAAGAUGGUAUCUGCGGGAUCUCCUCUGUUUCAAGAAUGGAAAACAUCAUGUGGAGAUCAGUAGAAGGGGAGCUCAACGCAAUCCUGGAAGAGAAUGGAGUUCAACUGACGGUCGUUGUGGGAUCUGUAAAAAACCCCAUGUGGAGAGGUCCACAGAGAUUGCCCGUGCCUGUGAACGAGCUGCCCCACGGCUGGAAGGCUUGGGGGAAAUCGUACUUCGUCAGAGCAGCAAAGACAAAUAACAGCUUUGUCGUGGAUGGUGACACACUGAAGGAAUGCCCACUCAAACAUAGAGCAUGGAACAGCUUUCUUGUGGAGGAUCAUGGGUUCGGGGUAUUUCACACUAGUGUCUGGCUCAAGGUUAGAGAAGAUUAUUCAUUAGAGUGUGAUCCAGCCGUUAUUGGAACAGCUGUUAAGGGAAAGGAGGCUGUACACAGUGAUCUAGGCUACUGGAUUGAGAGUGAGAAGAAUGACACAUGGAGGCUGAAGAGGGCCCAUCUGAUCGAGAUGAAAACAUGUGAAUGGCCAAAGUCCCACACAUUGUGGACAGAUGGAAUAGAAGAGAGUGAUCUGAUCAUACCCAAGUCUUUAGCUGGGCCACUCAGCCAUCACAAUACCAGAGAGGGCUACAGGACCCAAAUGAAAGGGCCAUGGCACAGUGAAGAGCUUGAAAUUCGGUUUGAGGAAUGCCCAGGCACUAAGGUCCACGUGGAGGAAACAUGUGGAACGAGAGGACCAUCUCUGAGAUCAACCACUGCAAGCGGAAGGGUGAUCGAGGAAUGGUGCUGCAGGGAGUGCACAAUGCCCCCACUGUCGUUCCGGGCUAAAGAUGGCUGUUGGUAUGGAAUGGAGAUAAGGCCCAGGAAAGAACCAGAAAGCAACUUAGUAAGGUCAAUGGUGACUGCAGGAUCAACUGAUCACAUGGACCACUUCUCCCUUGGAGUGCUUGUGAUUCUGCUCAUGGUGCAGGAAGGGUUGAAGAAGAGAAUGACCACAAAGAUCAUCAUAAGCACAUCAAUGGCAGUGCUGGUAGCUAUGAUCCUGGGAGGAUUUUCAAUGAGUGACCUGGCUAAGCUUGCAAUUUUGAUGGGUGCCACCUUCGCGGAAAUGAACACUGGAGGAGAUGUAGCUCAUCUGGCGCUGAUAGCGGCAUUCAAAGUCAGACCAGCGUUGCUGGUAUCUUUCAUCUUCAGAGCUAAUUGGACACCCCGUGAAAGCAUGCUGCUGGCCUUGGCCUCGUGUCUUUUGCAAACUGCGAUCUCCGCCUUGGAAGGCGACCUGAUGGUUCUCAUCAAUGGUUUUGCUUUGGCCUGGUUGGCAAUACGAGCGAUGGUUGUUCCACGCACUGAUAACAUCACCUUGGCAAUCCUGGCUGCUCUGACACCACUGGCCCGGGGCACACUGCUUGUGGCGUGGAGAGCAGGCCUUGCUACUUGCGGGGGGUUUAUGCUCCUCUCUCUGAAGGGAAAAGGCAGUGUGAAGAAGAACUUACCAUUUGUCAUGGCCCUGGGACUAACCGCUGUGAGGCUGGUCGACCCCAUCAACGUGGUGGGACUGCUGUUGCUCACAAGGAGUGGGAAGCGGAGCUGGCCCCCUAGCGAAGUACUCACAGCUGUUGGCCUGAUAUGCGCAUUGGCUGGAGGGUUCGCCAAGGCAGAUAUAGAGAUGGCUGGGCCCAUGGCCGCGGUCGGUCUGCUAAUUGUCAGUUACGUGGUCUCAGGAAAGAGUGUGGACAUGUACAUUGAAAGAGCAGGUGACAUCACAUGGGAAAAAGAUGCGGAAGUCACUGGAAACAGUCCCCGGCUCGAUGUGGCGCUAGAUGAGAGUGGUGAUUUCUCCCUGGUGGAGGAUGACGGUCCCCCCAUGAGAGAGAUCAUACUCAAGGUGGUCCUGAUGACCAUCUGUGGCAUGAACCCAAUAGCCAUACCCUUUGCAGCUGGAGCGUGGUACGUAUACGUGAAGACUGGAAAAAGGAGUGGUGCUCUAUGGGAUGUGCCUGCUCCCAAGGAAGUAAAAAAGGGGGAGACCACAGAUGGAGUGUACAGAGUAAUGACUCGUAGACUGCUAGGUUCAACACAAGUUGGAGUGGGAGUUAUGCAAGAGGGGGUCUUUCACACUAUGUGGCACGUCACAAAAGGAUCCGCGCUGAGAAGCGGUGAAGGGAGACUUGAUCCAUACUGGGGAGAUGUCAAGCAGGAUCUGGUGUCAUACUGUGGUCCAUGGAAGCUAGAUGCCGCCUGGGACGGGCACAGCGAGGUGCAGCUCUUGGCCGUGCCCCCCGGAGAGAGAGCGAGGAACAUCCAGACUCUGCCCGGAAUAUUUAAGACAAAGGAUGGGGACAUUGGAGCGGUUGCGCUGGAUUACCCAGCAGGAACUUCAGGAUCUCCUAUCCUAGACAAGUGUGGGAGAGUGAUAGGACUUUAUGGCAAUGGGGUCGUGAUCAAAAAUGGGAGUUAUGUUAGUGCCAUCACCCAAGGGAGGAGGGAGGAAGAGACUCCUGUUGAGUGCUUCGAGCCUUCGAUGCUGAAGAAGAAGCAGCUAACUGUCUUAGACUUGCAUCCUGGAGCUGGGAAAACCAGGAGAGUUCUUCCUGAAAUAGUCCGUGAAGCCAUAAAAACAAGACUCCGUACUGUGAUCUUAGCUCCAACCAGGGUUGUCGCUGCUGAAAUGGAGGAGGCCCUUAGAGGGCUUCCAGUGCGUUAUAUGACAACAGCAGUCAAUGUCACCCACUCUGGAACAGAAAUCGUCGACUUAAUGUGCCAUGCCACCUUCACUUCGCGUCUACUACAGCCAAUCAGAGUCCCCAACUAUAAUCUGUAUAUUAUGGAUGAGGCCCACUUCACAGAUCCCUCAAGUAUAGCAGCAAGAGGAUACAUUUCAACAAGGGUUGAGAUGGGCGAGGCGGCCGCCAUCUUCAUGACCGCCACGCCACCAGGAACCCGUGACGCAUUUCCGGACUCCAACUCACCAAUUAUGGACACCGAAGUGGAAGUCCCAGAGAGAGCCUGGAGCUCAGGCUUUGAUUGGGUGACGGAUCAUUCUGGAAAAACAGUUUGGUUUGUUCCAAGCGUGAGGAACGGCAAUGAGAUCGCAGCUUGUCUGACAAAGGCUGGAAAACGGGUCAUACAGCUCAGCAGAAAGACUUUUGAGACAGAGUUCCAGAAAACAAAACAUCAAGAGUGGGACUUUGUCGUGACAACUGACAUUUCAGAGAUGGGCGCCAACUUUAAAGCUGACCGUGUCAUAGAUUCCAGGAGAUGCCUAAAGCCGGUCAUACUUGAUGGCGAGAGAGUCAUUCUGGCUGGACCCAUGCCUGUCACACAUGCCAGCGCUGCCCAGAGGAGGGGGCGCAUAGGCAGGAAUCCCAACAAACCUGGAGAUGAGUAUCUGUAUGGAGGUGGGUGCGCAGAGACUGACGAAGACCAUGCACACUGGCUUGAAGCAAGAAUGCUCCUUGACAAUAUUUACCUCCAAGAUGGCCUCAUAGCCUCGCUCUAUCGACCUGAGGCCGACAAAGUAGCAGCCAUUGAGGGAGAGUUCAAGCUUAGGACGGAGCAAAGGAAGACCUUUGUGGAACUCAUGAAAAGAGGAGAUCUUCCUGUUUGGCUGGCCUAUCAGGUUGCAUCUGCCGGAAUAACCUACACAGAUAGAAGAUGGUGCUUUGAUGGCACGACCAACAACACCAUAAUGGAAGACAGUGUGCCGGCAGAAGUGUGGACCAGACACGGAGAGAAAAGAGUGCUCAAACCGAGGUGGAUGGACGCCAGAGUUUGUUCAGAUCAUGCGGCCCUGAAGUCAUUCAAGGAGUUUGCCGCUGGGAAAAGAGGAGCGGCUUUUGGAGUGAUGGAAGCCCUGGGAACACUGCCAGGACACAUGACAGAGAGAUUCCAGGAAGCCAUUGACAACCUCGCUGUGCUCAUGCGGGCAGAGACUGGAAGCAGGCCUUACAAAGCCGCGGCGGCCCAAUUGCCGGAGACCCUAGAGACCAUUAUGCUUUUGGGGUUGCUGGGAACAGUCUCGCUGGGAAUCUUCUUCGUCUUGAUGAGGAACAAGGGCAUAGGGAAGAUGGGCUUUGGAAUGGUGACUCUUGGGGCCAGCGCAUGGCUCAUGUGGCUCUCGGAAAUUGAGCCAGCCAGAAUUGCAUGUGUCCUCAUUGUUGUGUUCCUAUUGCUGGUGGUGCUCAUACCUGAGCCAGAAAAGCAAAGAUCUCCCCAGGACAACCAAAUGGCAAUCAUCAUCAUGGUAGCAGUAGGUCUUCUGGGCUUGAUUACCGCCAAUGAACUCGGAUGGUUGGAGAGAACAAAGAGUGACCUAAGCCAUCUAAUGGGAAGGAGAGAGGAGGGGGCAACCAUAGGAUUCUCAAUGGACAUUGACCUGCGGCCAGCCUCAGCUUGGGCCAUCUAUGCUGCCUUGACAACUUUCAUUACCCCAGCCGUCCAACAUGCAGUGACCACCUCAUACAACAACUACUCCUUAAUGGCGAUGGCCACGCAAGCUGGAGUGUUGUUUGGUAUGGGCAAAGGGAUGCCAUUCUACGCAUGGGACUUUGGAGUCCCGCUGCUAAUGAUAGGUUGCUACUCACAAUUAACACCCCUGACCCUAAUAGUGGCCAUCAUUUUGCUCGUGGCGCACUACAUGUACUUGAUCCCAGGGCUGCAGGCAGCAGCUGCGCGUGCUGCCCAGAAGAGAACGGCAGCUGGCAUCAUGAAGAACCCUGUUGUGGAUGGAAUAGUGGUGACUGACAUUGACACAAUGACAAUUGACCCCCAAGUGGAGAAAAAGAUGGGACAGGUGCUACUCAUAGCAGUAGCCGUCUCCAGCGCCAUACUGUCGCGGACCGCCUGGGGGUGGGGGGAGGCUGGGGCCCUGAUCACAGCCGCAACUUCCACUUUGUGGGAAGGCUCUCCGAACAAGUACUGGAACUCCUCUACAGCCACUUCACUGUGUAACAUUUUUAGGGGAAGUUACUUGGCUGGAGCUUCUCUAAUCUACACAGUAACAAGAAACGCUGGCUUGGUCAAGAGACGUGGGGGUGGAACAGGAGAGACCCUGGGAGAGAAAUGGAAGGCCCGCUUGAACCAGAUGUCGGCCCUGGAGUUCUACUCCUACAAAAAGUCAGGCAUCACCGAGGUGUGCAGAGAAGAGGCCCGCCGCGCCCUCAAGGACGGUGUGGCAACGGGAGGCCAUGCUGUGUCCCGAGGAAGUGCAAAGCUGAGAUGGUUGGUGGAGCGGGGAUACCUGCAGCCCUAUGGAAAGGUCAUUGAUCUUGGAUGUGGCAGAGGGGGCUGGAGUUACUACGCCGCCACCAUCCGCAAAGUUCAAGAAGUGAAAGGAUACACAAAAGGAGGCCCUGGUCAUGAAGAACCCGUGUUGGUGCAAAGCUAUGGGUGGAACAUAGUCCGUCUUAAGAGUGGGGUGGACGUCUUUCAUAUGGCGGCUGAGCCGUGUGACACGUUGCUGUGUGACAUAGGUGAGUCAUCAUCUAGUCCUGAAGUGGAAGAAGCACGGACGCUCAGAGUCCUCUCCAUGGUGGGGGAUUGGCUUGAAAAAAGACCAGGAGCCUUUUGUAUAAAAGUGUUGUGCCCAUACACCAGCACUAUGAUGGAAACCCUGGAGCGACUGCAGCGUAGGUAUGGGGGAGGACUGGUCAGAGUGCCACUCUCCCGCAACUCUACACAUGAGAUGUACUGGGUCUCUGGAGCGAAAAGCAACACCAUAAAAAGUGUGUCCACCACGAGCCAGCUCCUCUUGGGGCGCAUGGACGGGCCUAGGAGGCCAGUGAAAUAUGAGGAGGAUGUGAAUCUCGGCUCUGGCACGCGGGCUGUGGUAAGCUGCGCUGAAGCUCCCAACAUGAAGAUCAUUGGUAACCGCAUUGAAAGGAUCCGCAGUGAGCACGCGGAAACGUGGUUCUUUGACGAGAACCACCCAUAUAGGACAUGGGCUUACCAUGGAAGCUAUGAGGCCCCCACACAAGGGUCAGCGUCCUCUCUAAUAAACGGGGUUGUCAGGCUCCUGUCAAAACCCUGGGAUGUGGUGACUGGAGUCACAGGAAUAGCCAUGACCGACACCACACCGUAUGGUCAGCAAAGAGUUUUCAAGGAAAAAGUGGACACUAGGGUGCCAGACCCCCAAGAAGGCACUCGUCAGGUUAUGAGCAUGGUCUCUUCCUGGUUGUGGAAAGAGCUAGGCAAACACAAACGGCCACGAGUCUGUACCAAAGAAGAGUUCAUCAACAAGGUUCGUAGCAAUGCAGCAUUAGGGGCAAUAUUUGAAGAGGAAAAAGAGUGGAAGACUGCAGUGGAAGCUGUGAACGAUCCAAGGUUCUGGGCUCUAGUGGACAAGGAAAGAGAGCACCACCUGAGAGGAGAGUGCCAGAGUUGUGUGUACAACAUGAUGGGAAAAAGAGAAAAGAAACAAGGGGAAUUUGGAAAGGCCAAGGGCAGCCGCGCCAUCUGGUAUAUGUGGCUAGGGGCUAGAUUUCUAGAGUUCGAAGCCCUUGGAUUCUUGAACGAGGAUCACUGGAUGGGGAGAGAGAACUCAGGAGGUGGUGUUGAAGGGCUGGGAUUACAAAGACUCGGAUAUGUCCUAGAAGAGAUGAGUCGUAUACCAGGAGGAAGGAUGUAUGCAGAUGACACUGCUGGCUGGGACACCCGCAUUAGCAGGUUUGAUCUGGAGAAUGAAGCUCUAAUCACCAACCAAAUGGAGAAAGGGCACAGGGCCUUGGCAUUGGCCAUAAUCAAGUACACAUACCAAAACAAAGUGGUAAAGGUCCUUAGACCAGCUGAAAAAGGGAAAACAGUUAUGGACAUUAUUUCGAGACAAGACCAAAGGGGGAGCGGACAAGUUGUCACUUACGCUCUUAACACAUUUACCAACCUAGUGGUGCAACUCAUUCGGAAUAUGGAGGCUGAGGAAGUUCUAGAGAUGCAAGACUUGUGGCUGCUGCGGAGGUCAGAGAAAGUGACUAACUGGUUGCAGAGCAACGGAUGGGAUAGGCUCAAACGAAUGGCAGUCAGUGGAGAUGAUUGCGUUGUGAAGCCAAUUGAUGAUAGGUUUGCACAUGCCCUCAGGUUCUUGAAUGAUAUGGGAAAAGUUAGGAAGGACACACAAGAGUGGAAACCCUCAACUGGAUGGGACAACUGGGAAGAAGUUCCGUUUUGCUCCCACCACUUCAACAAGCUCCAUCUCAAGGACGGGAGGUCCAUUGUGGUUCCCUGCCGCCACCAAGAUGAACUGAUUGGCCGGGCCCGCGUCUCUCCAGGGGCGGGAUGGAGCAUCCGGGAGACUGCUUGCCUAGCAAAAUCAUAUGCGCAAAUGUGGCAGCUCCUUUAUUUCCACAGAAGGGACCUCCGACUGAUGGCCAAUGCCAUUUGUUCAUCUGUGCCAGUUGACUGGGUUCCAACUGGGAGAACUACCUGGUCAAUCCAUGGAAAGGGAGAAUGGAUGACCACUGAAGACAUGCUUGUGGUGUGGAACAGAGUGUGGAUUGAGGAGAACGACCACAUGGAAGACAAGACCCCAGUUACGAAAUGGACAGACAUUCCCUAUUUGGGAAAAAGGGAAGACUUGUGGUGUGGAUCUCUCAUAGGGCACAGACCGCGCACCACCUGGGCUGAGAACAUUAAAAACACAGUCAACAUGGUGCGCAGGAUCAUAGGUGAUGAAGAAAAGUACAUGGACUACCUAUCCACCCAAGUUCGCUACUUGGGUGAAGAAGGGUCUACACCUGGAGUGCUGUAAGCACCAAUCUUAAUGUUGUCAGGCCUGCUAGUCAGCCACAGCUUGGGGAAAGCUGUGCAGCC (SEQ ID NO: 746) MR 766AGUUGUUGAUCUGUGUGAGUCAGACUGCGACAGUUCGAGUCUGAAGCGAGAGC Zika virusUAACAACAGUAUCAACAGGUUUAAUUUGGAUUUGGAAACGAGAGUUUCUGGU genome,CAUGAAAAACCCCAAAGAAGAAAUCCGGAGGAUCCGGAUUGUCAAUAUGCUAA UgandaAACGCGGAGUAGCCCGUGUAAACCCCUUGGGAGGUUUGAAGAGGUUGCCAGCC 1947GGACUUCUGCUGGGUCAUGGACCCAUCAGAAUGGUUUUGGCGAUACUAGCCUU (AccessionUUUGAGAUUUACAGCAAUCAAGCCAUCACUGGGCCUUAUCAACAGAUGGGGUU number:CCGUGGGGAAAAAAGAGGCUAUGGAAAUAAUAAAGAAGUUCAAGAAAGAUCU AY632535;UGCUGCCAUGUUGAGAAUAAUCAAUGCUAGGAAAGAGAGGAAGAGACGUGGC 10,794-nts)GCAGACACCAGCAUCGGAAUCAUUGGCCUCCUGCUGACUACAGCCAUGGCAGCAGAGAUCACUAGACGCGGGAGUGCAUACUACAUGUACUUGGAUAGGAGCGAUGCCGGGAAGGCCAUUUCGUUUGCUACCACAUUGGGAGUGAACAAGUGCCACGUACAGAUCAUGGACCUCGGGCACAUGUGUGACGCCACCAUGAGUUAUGAGUGCCCUAUGCUGGAUGAGGGAGUGGAACCAGAUGAUGUCGAUUGCUGGUGCAACACGACAUCAACUUGGGUUGUGUACGGAACCUGUCAUCACAAAAAAGGUGAGGCACGGCGAUCUAGAAGAGCCGUGACGCUCCCUUCUCACUCUACAAGGAAGUUGCAAACGCGGUCGCAGACCUGGUUAGAAUCAAGAGAAUACACGAAGCACUUGAUCAAGGUUGAAAACUGGAUAUUCAGGAACCCCGGGUUUGCGCUAGUGGCCGUUGCCAUUGCCUGGCUUUUGGGAAGCUCGACGAGCCAAAAAGUCAUAUACUUGGUCAUGAUACUGCUGAUUGCCCCGGCAUACAGUAUCAGGUGCAUUGGAGUCAGCAAUAGAGACUUCGUGGAGGGCAUGUCAGGUGGGACCUGGGUUGAUGUUGUCUUGGAACAUGGAGGCUGCGUUACCGUGAUGGCACAGGACAAGCCAACAGUCGACAUAGAGUUGGUCACGACGACGGUUAGUAACAUGGCCGAGGUAAGAUCCUAUUGCUACGAGGCAUCGAUAUCGGACAUGGCUUCGGACAGUCGUUGCCCAACACAAGGUGAAGCCUACCUUGACAAGCAAUCAGACACUCAAUAUGUCUGCAAAAGAACAUUAGUGGACAGAGGUUGGGGAAACGGUUGUGGACUUUUUGGCAAAGGGAGCUUGGUGACAUGUGCCAAGUUUACGUGUUCUAAGAAGAUGACCGGGAAGAGCAUUCAACCGGAAAAUCUGGAGUAUCGGAUAAUGCUAUCAGUGCAUGGCUCCCAGCAUAGCGGGAUGAUUGGAUAUGAAACUGACGAAGAUAGAGCGAAAGUCGAGGUUACGCCUAAUUCACCAAGAGCGGAAGCAACCUUGGGAGGCUUUGGAAGCUUAGGACUUGACUGUGAACCAAGGACAGGCCUUGACUUUUCAGAUCUGUAUUACCUGACCAUGAACAAUAAGCAUUGGUUGGUGCACAAAGAGUGGUUUCAUGACAUCCCAUUGCCUUGGCAUGCUGGGGCAGACACCGGAACUCCACACUGGAACAACAAAGAGGCAUUGGUAGAAUUCAAGGAUGCCCACGCCAAGAGGCAAACCGUCGUCGUUCUGGGGAGCCAGGAAGGAGCCGUUCACACGGCUCUCGCUGGAGCUCUAGAGGCUGAGAUGGAUGGUGCAAAGGGAAGGCUGUUCUCUGGCCAUUUGAAAUGCCGCCUAAAAAUGGACAAGCUUAGAUUGAAGGGCGUGUCAUAUUCCUUGUGCACUGCGGCAUUCACAUUCACCAAGGUCCCAGCUGAAACACUGCAUGGAACAGUCACAGUGGAGGUGCAGUAUGCAGGGACAGAUGGACCCUGCAAGAUCCCAGUCCAGAUGGCGGUGGACAUGCAGACCCUGACCCCAGUUGGAAGGCUGAUAACCGCCAACCCCGUGAUUACUGAAAGCACUGAGAACUCAAAGAUGAUGUUGGAGCUUGACCCACCAUUUGGGGAUUCUUACAUUGUCAUAGGAGUUGGGGACAAGAAAAUCACCCACCACUGGCAUAGGAGUGGUAGCACCAUCGGAAAGGCAUUUGAGGCCACUGUGAGAGGCGCCAAGAGAAUGGCAGUCCUGGGGGAUACAGCCUGGGACUUCGGAUCAGUCGGGGGUGUGUUCAACUCACUGGGUAAGGGCAUUCACCAGAUUUUUGGAGCAGCCUUCAAAUCACUGUUUGGAGGAAUGUCCUGGUUCUCACAGAUCCUCAUAGGCACGCUGCUAGUGUGGUUAGGUUUGAACACAAAGAAUGGAUCUAUCUCCCUCACAUGCUUGGCCCUGGGGGGAGUGAUGAUCUUCCUCUCCACGGCUGUUUCUGCUGACGUGGGGUGCUCAGUGGACUUCUCAAAAAAGGAAACGAGAUGUGGCACGGGGGUAUUCAUCUAUAAUGAUGUUGAAGCCUGGAGGGACCGGUACAAGUACCAUCCUGACUCCCCCCGCAGAUUGGCAGCAGCAGUCAAGCAGGCCUGGGAAGAGGGGAUCUGUGGGAUCUCAUCCGUUUCAAGAAUGGAAAACAUCAUGUGGAAAUCAGUAGAAGGGGAGCUCAAUGCUAUCCUAGAGGAGAAUGGAGUUCAACUGACAGUUGUUGUGGGAUCUGUAAAAAACCCCAUGUGGAGAGGUCCACAAAGAUUGCCAGUGCCUGUGAAUGAGCUGCCCCAUGGCUGGAAAGCCUGGGGGAAAUCGUAUUUUGUUAGGGCGGCAAAGACCAACAACAGUUUUGUUGUCGACGGUGACACACUGAAGGAAUGUCCGCUUGAGCACAGAGCAUGGAAUAGUUUUCUUGUGGAGGAUCACGGGUUUGGAGUCUUCCACACCAGUGUCUGGCUUAAGGUCAGAGAAGAUUACUCAUUAGAAUGUGACCCAGCCGUCAUAGGAACAGCUGUUAAGGGAAGGGAGGCCGCGCACAGUGAUCUGGGCUAUUGGAUUGAAAGUGAAAAGAAUGACACAUGGAGGCUGAAGAGGGCCCACCUGAUUGAGAUGAAAACAUGUGAAUGGCCAAAGUCUCACACAUUGUGGACAGAUGGAGUAGAAGAAAGUGAUCUUAUCAUACCCAAGUCUUUAGCUGGUCCACUCAGCCACCACAACACCAGAGAGGGUUACAGAACCCAAGUGAAAGGGCCAUGGCACAGUGAAGAGCUUGAAAUCCGGUUUGAGGAAUGUCCAGGCACCAAGGUUUACGUGGAGGAGACAUGCGGAACUAGAGGACCAUCUCUGAGAUCAACUACUGCAAGUGGAAGGGUCAUUGAGGAAUGGUGCUGUAGGGAAUGCACAAUGCCCCCACUAUCGUUUCGAGCAAAAGACGGCUGCUGGUAUGGAAUGGAGAUAAGGCCCAGGAAAGAACCAGAGAGCAACUUAGUGAGGUCAAUGGUGACAGCGGGGUCAACCGAUCAUAUGGACCACUUCUCUCUUGGAGUGCUUGUGAUUCUACUCAUGGUGCAGGAGGGGUUGAAGAAGAGAAUGACCACAAAGAUCAUCAUGAGCACAUCAAUGGCAGUGCUGGUAGUCAUGAUCUUGGGAGGAUUUUCAAUGAGUGACCUGGCCAAGCUUGUGAUCCUGAUGGGUGCUACUUUCGCAGAAAUGAACACUGGAGGAGAUGUAGCUCACUUGGCAUUGGUAGCGGCAUUUAAAGUCAGACCAGCCUUGCUGGUCUCCUUCAUUUUCAGAGCCAAUUGGACACCCCGUGAGAGCAUGCUGCUAGCCCUGGCUUCGUGUCUUCUGCAAACUGCGAUCUCUGCUCUUGAAGGUGACUUGAUGGUCCUCAUUAAUGGAUUUGCUUUGGCCUGGUUGGCAAUUCGAGCAAUGGCCGUGCCACGCACUGACAACAUCGCUCUACCAAUCUUGGCUGCUCUAACACCACUAGCUCGAGGCACACUGCUCGUGGCAUGGAGAGCGGGCCUGGCUACUUGUGGAGGGAUCAUGCUCCUCUCCCUGAAAGGGAAAGGUAGUGUGAAGAAGAACCUGCCAUUUGUCAUGGCCCUGGGAUUGACAGCUGUGAGGGUAGUAGACCCUAUUAAUGUGGUAGGACUACUGUUACUCACAAGGAGUGGGAAGCGGAGCUGGCCCCCUAGUGAAGUUCUCACAGCCGUUGGCCUGAUAUGUGCACUGGCCGGAGGGUUUGCCAAGGCAGACAUUGAGAUGGCUGGACCCAUGGCUGCAGUAGGCUUGCUAAUUGUCAGCUAUGUGGUCUCGGGAAAGAGUGUGGACAUGUACAUUGAAAGAGCAGGUGACAUCACAUGGGAAAAGGACGCGGAAGUCACUGGAAACAGUCCUCGGCUUGACGUGGCACUGGAUGAGAGUGGUGACUUCUCCUUGGUAGAGGAAGAUGGUCCACCCAUGAGAGAGAUCAUACUCAAGGUGGUCCUGAUGGCCAUCUGUGGCAUGAACCCAAUAGCUAUACCUUUUGCUGCAGGAGCGUGGUAUGUGUAUGUGAAGACUGGGAAAAGGAGUGGCGCCCUCUGGGACGUGCCUGCUCCCAAAGAAGUGAAGAAAGGAGAGACCACAGAUGGAGUGUACAGAGUGAUGACUCGCAGACUGCUAGGUUCAACACAGGUUGGAGUGGGAGUCAUGCAAGAGGGAGUCUUCCACACCAUGUGGCACGUUACAAAAGGAGCCGCACUGAGGAGCGGUGAGGGAAGACUUGAUCCAUACUGGGGGGAUGUCAAGCAGGACUUGGUGUCAUACUGUGGGCCUUGGAAGUUGGAUGCAGCUUGGGAUGGACUCAGCGAGGUACAGCUUUUGGCCGUACCUCCCGGAGAGAGGGCCAGAAACAUUCAGACCCUGCCUGGAAUAUUCAAGACAAAGGACGGGGACAUCGGAGCAGUUGCUCUGGACUACCCUGCAGGGACCUCAGGAUCUCCGAUCCUAGACAAAUGUGGAAGAGUGAUAGGACUCUAUGGCAAUGGGGUUGUGAUCAAGAAUGGAAGCUAUGUUAGUGCUAUAACCCAGGGAAAGAGGGAGGAGGAGACUCCGGUUGAAUGUUUCGAACCCUCGAUGCUGAAGAAGAAGCAGCUAACUGUCUUGGAUCUGCAUCCAGGAGCCGGAAAAACCAGGAGAGUUCUUCCUGAAAUAGUCCGUGAAGCCAUAAAAAAGAGACUCCGGACAGUGAUCUUGGCACCAACUAGGGUUGUCGCUGCUGAGAUGGAGGAGGCCUUGAGAGGACUUCCGGUGCGUUACAUGACAACAGCAGUCAACGUCACCCAUUCUGGGACAGAAAUCGUUGAUUUGAUGUGCCAUGCCACUUUCACUUCACGCUUACUACAACCCAUCAGAGUCCCUAAUUACAAUCUCAACAUCAUGGAUGAAGCCCACUUCACAGACCCCUCAAGUAUAGCUGCAAGAGGAUACAUAUCAACAAGGGUUGAAAUGGGCGAGGCGGCUGCCAUUUUUAUGACUGCCACACCACCAGGAACCCGUGAUGCGUUUCCUGACUCUAACUCACCAAUCAUGGACACAGAAGUGGAAGUCCCAGAGAGAGCCUGGAGCUCAGGCUUUGAUUGGGUGACAGACCAUUCUGGGAAAACAGUUUGGUUCGUUCCAAGCGUGAGAAACGGAAAUGAAAUCGCAGCCUGUCUGACAAAGGCUGGAAAGCGGGUCAUACAGCUCAGCAGGAAGACUUUUGAGACAGAAUUUCAGAAAACAAAAAAUCAAGAGUGGGACUUUGUCAUAACAACUGACAUCUCAGAGAUGGGCGCCAACUUCAAGGCUGACCGGGUCAUAGACUCUAGGAGAUGCCUAAAACCAGUCAUACUUGAUGGUGAGAGAGUCAUCUUGGCUGGGCCCAUGCCUGUCACGCAUGCUAGUGCUGCUCAGAGGAGAGGACGUAUAGGCAGGAACCCUAACAAACCUGGAGAUGAGUACAUGUAUGGAGGUGGGUGUGCAGAGACUGAUGAAGGCCAUGCACACUGGCUUGAAGCAAGAAUGCUUCUUGACAACAUCUACCUCCAGGAUGGCCUCAUAGCCUCGCUCUAUCGGCCUGAGGCCGAUAAGGUAGCCGCCAUUGAGGGAGAGUUUAAGCUGAGGACAGAGCAAAGGAAGACCUUCGUGGAACUCAUGAAGAGAGGAGACCUUCCCGUCUGGCUAGCCUAUCAGGUUGCAUCUGCCGGAAUAACUUACACAGACAGAAGAUGGUGCUUUGAUGGCACAACCAACAACACCAUAAUGGAAGACAGUGUACCAGCAGAGGUUUGGACAAAGUAUGGAGAGAAGAGAGUGCUCAAACCGAGAUGGAUGGAUGCUAGGGUCUGUUCAGACCAUGCGGCCCUGAAGUCGUUCAAAGAAUUCGCCGCUGGAAAAAGAGGAGCGGCUUUGGGAGUAAUGGAGGCCCUGGGAACACUGCCAGGACACAUGACAGAGAGGUUUCAGGAAGCCAUUGACAACCUCGCCGUGCUCAUGCGAGCAGAGACUGGAAGCAGGCCUUAUAAGGCAGCGGCAGCCCAACUGCCGGAGACCCUAGAGACCAUUAUGCUCUUAGGUUUGCUGGGAACAGUUUCACUGGGGAUCUUCUUCGUCUUGAUGCGGAAUAAGGGCAUCGGGAAGAUGGGCUUUGGAAUGGUAACCCUUGGGGCCAGUGCAUGGCUCAUGUGGCUUUCGGAAAUUGAACCAGCCAGAAUUGCAUGUGUCCUCAUUGUUGUGUUUUUAUUACUGGUGGUGCUCAUACCCGAGCCAGAGAAGCAAAGAUCUCCCCAAGAUAACCAGAUGGCAAUUAUCAUCAUGGUGGCAGUGGGCCUUCUAGGUUUGAUAACUGCAAACGAACUUGGAUGGCUGGAAAGAACAAAAAAUGACAUAGCUCAUCUAAUGGGAAGGAGAGAAGAAGGAGCAACCAUGGGAUUCUCAAUGGACAUUGAUCUGCGGCCAGCCUCCGCCUGGGCUAUCUAUGCCGCAUUGACAACUCUCAUCACCCCAGCUGUCCAACAUGCGGUAACCACUUCAUACAACAACUACUCCUUAAUGGCGAUGGCCACACAAGCUGGAGUGCUGUUUGGCAUGGGCAAAGGGAUGCCAUUUAUGCAUGGGGACCUUGGAGUCCCGCUGCUAAUGAUGGGUUGCUAUUCACAAUUAACACCCCUGACUCUGAUAGUAGCUAUCAUUCUGCUUGUGGCGCACUACAUGUACUUGAUCCCAGGCCUACAAGCGGCAGCAGCGCGUGCUGCCCAGAAAAGGACAGCAGCUGGCAUCAUGAAGAAUCCCGUUGUGGAUGGAAUAGUGGUAACUGACAUUGACACAAUGACAAUAGACCCCCAGGUGGAGAAGAAGAUGGGACAAGUGUUACUCAUAGCAGUAGCCAUCUCCAGUGCUGUGCUGCUGCGGACCGCCUGGGGAUGGGGGGAGGCUGGAGCUCUGAUCACAGCAGCGACCUCCACCUUGUGGGAAGGCUCUCCAAACAAAUACUGGAACUCCUCUACAGCCACCUCACUGUGCAACAUCUUCAGAGGAAGCUAUCUGGCAGGAGCUUCCCUUAUCUAUACAGUGACGAGAAACGCUGGCCUGGUUAAGAGACGUGGAGGUGGGACGGGAGAGACUCUGGGAGAGAAGUGGAAAGCUCGUCUGAAUCAGAUGUCGGCCCUGGAGUUCUACUCUUAUAAAAAGUCAGGUAUCACUGAAGUGUGUAGAGAGGAGGCUCGCCGUGCCCUCAAGGAUGGAGUGGCCACAGGAGGACAUGCCGUAUCCCGGGGAAGUGCAAAGAUCAGAUGGUUGGAGGAGAGAGGAUAUCUGCAGCCCUAUGGGAAGGUUGUUGACCUCGGAUGUGGCAGAGGGGGCUGGAGCUAUUAUGCCGCCACCAUCCGCAAAGUGCAGGAGGUGAGAGGAUACACAAAGGGAGGUCCCGGUCAUGAAGAACCCAUGCUGGUGCAAAGCUAUGGGUGGAACAUAGUUCGUCUCAAGAGUGGAGUGGACGUCUUCCACAUGGCGGCUGAGCCGUGUGACACUCUGCUGUGUGACAUAGGUGAGUCAUCAUCUAGUCCUGAAGUGGAAGAGACACGAACACUCAGAGUGCUCUCUAUGGUGGGGGACUGGCUUGAAAAAAGACCAGGGGCCUUCUGUAUAAAGGUGCUGUGCCCAUACACCAGCACUAUGAUGGAAACCAUGGAGCGACUGCAACGUAGGCAUGGGGGAGGAUUAGUCAGAGUGCCAUUGUGUCGCAACUCCACACAUGAGAUGUACUGGGUCUCUGGGGCAAAGAGCAACAUCAUAAAAAGUGUGUCCACCACAAGUCAGCUCCUCCUGGGACGCAUGGAUGGCCCCAGGAGGCCAGUGAAAUAUGAGGAGGAUGUGAACCUCGGCUCGGGUACACGAGCUGUGGCAAGCUGUGCUGAGGCUCCUAACAUGAAAAUCAUCGGCAGGCGCAUUGAGAGAAUCCGCAAUGAACAUGCAGAAACAUGGUUUCUUGAUGAAAACCACCCAUACAGGACAUGGGCCUACCAUGGGAGCUACGAAGCCCCCACGCAAGGAUCAGCGUCUUCCCUCGUGAACGGGGUUGUUAGACUCCUGUCAAAGCCUUGGGACGUGGUGACUGGAGUUACAGGAAUAGCCAUGACUGACACCACACCAUACGGCCAACAAAGAGUCUUCAAAGAAAAAGUGGACACCAGGGUGCCAGAUCCCCAAGAAGGCACUCGCCAGGUAAUGAACAUAGUCUCUUCCUGGCUGUGGAAGGAGCUGGGGAAACGCAAGCGGCCACGCGUCUGCACCAAAGAAGAGUUUAUCAACAAGGUGCGCAGCAAUGCAGCACUGGGAGCAAUAUUUGAAGAGGAAAAAGAAUGGAAGACGGCUGUGGAAGCUGUGAAUGAUCCAAGGUUUUGGGCCCUAGUGGAUAGGGAGAGAGAACACCACCUGAGAGGAGAGUGUCACAGCUGUGUGUACAACAUGAUGGGAAAAAGAGAAAAGAAGCAAGGAGAGUUCGGGAAAGCAAAAGGUAGCCGCGCCAUCUGGUACAUGUGGUUGGGAGCCAGAUUCUUGGAGUUUGAAGCCCUUGGAUUCUUGAACGAGGACCAUUGGAUGGGAAGAGAAAACUCAGGAGGUGGAGUCGAAGGGUUAGGAUUGCAAAGACUUGGAUACAUUCUAGAAGAAAUGAAUCGGGCACCAGGAGGAAAGAUGUACGCAGAUGACACUGCUGGCUGGGACACCCGCAUUAGUAAGUUUGAUCUGGAGAAUGAAGCUCUGAUUACCAACCAAAUGGAGGAAGGGCACAGAACUCUGGCGUUGGCCGUGAUUAAAUACACAUACCAAAACAAAGUGGUGAAGGUUCUCAGACCAGCUGAAGGAGGAAAAACAGUUAUGGACAUCAUUUCAAGACAAGACCAGAGAGGGAGUGGACAAGUUGUCACUUAUGCUCUCAACACAUUCACCAACUUGGUGGUGCAGCUUAUCCGGAACAUGGAAGCUGAGGAAGUGUUAGAGAUGCAAGACUUAUGGUUGUUGAGGAAGCCAGAGAAAGUGACCAGAUGGUUGCAGAGCAAUGGAUGGGAUAGACUCAAACGAAUGGCGGUCAGUGGAGAUGACUGCGUUGUGAAGCCAAUCGAUGAUAGGUUUGCACAUGCCCUCAGGUUCUUGAAUGACAUGGGAAAAGUUAGGAAAGACACACAGGAGUGGAAACCCUCGACUGGAUGGAGCAAUUGGGAAGAAGUCCCGUUCUGCUCCCACCACUUCAACAAGCUGUACCUCAAGGAUGGGAGAUCCAUUGUGGUCCCUUGCCGCCACCAAGAUGAACUGAUUGGCCGAGCUCGCGUCUCACCAGGGGCAGGAUGGAGCAUCCGGGAGACUGCCUGUCUUGCAAAAUCAUAUGCGCAGAUGUGGCAGCUCCUUUAUUUCCACAGAAGAGACCUUCGACUGAUGGCUAAUGCCAUUUGCUCGGCUGUGCCAGUUGACUGGGUACCAACUGGGAGAACCACCUGGUCAAUCCAUGGAAAGGGAGAAUGGAUGACCACUGAGGACAUGCUCAUGGUGUGGAAUAGAGUGUGGAUUGAGGAGAACGACCAUAUGGAGGACAAGACUCCUGUAACAAAAUGGACAGACAUUCCCUAUCUAGGAAAAAGGGAGGACUUAUGGUGUGGAUCCCUUAUAGGGCACAGACCCCGCACCACUUGGGCUGAAAACAUCAAAGACACAGUCAACAUGGUGCGCAGGAUCAUAGGUGAUGAAGAAAAGUACAUGGACUAUCUAUCCACCCAAGUCCGCUACUUGGGUGAGGAAGGGUCCACACCCGGAGUGUUGUAAGCACCAAUUUUAGUGUUGUCAGGCCUGCUAGUCAGCCACAGUUUGGGGAAAGCUGUGCAGCCUGUAACCCCCCCAGGAGAAGCUGGGAAACCAAGCUCAUAGUCAGGCCGAGAACGCCAUGGCACGGAAGAAGCCAUGCUGCCUGUGAGCCCCUCAGAGGACACUGAGUCAAAAAACCCCACGCGCUUGGAAGCGCAGGAUGGGAAAAGAAGGUGGCGACCUUCCCCACCCUUCAAUCUGGGGCCUGAACUGGAGACUAGCUGUGAAUCUCCAGCAGAGGGACUAGUGGUUAGAGGAGACCCCCCGGAAAACGCAAAACAGCAUAUUGACGUGGGAAAGACCAGAGACUCCAUGAGUUUCCACCACGCUGGCCGCCAGGCACAGAUCGCCGAACUUCGGCGGCCGGUGUGGGGAAAUCCAUGGUUUCU (SEQ ID NO: 747)

TABLE 8  Sequences of Toehold Switch Sensors Used for Zika RNA DetectionToehold Toehold Switch RNA Sequences Switch for Detection of Zika VirusTarget Sequence in Zika Virus Name from the Americas (KU312312)from the Americas (KU312312) 27B_N1 GGGUUUCGCUCUAUUCUCAUCAGUGACACAGGACAUGAAACUGAUGAGA UUCAUGUCCUGUGUCGGACUUUAGAUAGAGCGAAA (SEQ ID NO: 758) AACAGAGGAGAUAAAGAUGGACACAGGACACAACCUGGCGGCAGCGCA AAAG (SEQ ID NO: 748) 27B_N2GGGCUCAACUUUCGCUCUAUUCUC GGACAUGAAACUGAUGAGAAUAGAAUCAGUUUCAUGUCCGGACUUUAG GCGAAAGUUGAG (SEQ ID NO: 759)AACAGAGGAGAUAAAGAUGGGACA UGAAACAACCUGGCGGCAGCGCAA GAAG (SEQ ID NO: 749)27B_N3 GGGUUAUCUCAACUUUCGCUCUAU AUGAAACUGAUGAGAAUAGAGCGAUCUCAUCAGUUUCAUGGACUUUAG AAGUUGAGAUAA (SEQ ID NO: 760)AACAGAGGAGAUAAAGAUGAUGAA ACUGAUAACCUGGCGGCAGCGCAA GAAG (SEQ ID NO: 750)27B_N4 GGGUCGCUCUAUUCUCAUCAGUUU AUGACACAGGACAUGAAACUGAUGACAUGUCCUGUGUCAUGGACUUUAG GAAUAGAGCGA (SEQ ID NO: 761)AACAGAGGAGAUAAAGAUGAUGAC ACAGGAAACCUGGCGGCAGCGCAA GAAG (SEQ ID NO: 751)27B_N5 GGGUGGCUUCGGCUCUUGGUGAAU GAGAUAACGCCCAAUUCACCAAGAGUGGGCGUUAUCUCGGACUUUAGAA CCGAAGCCACC (SEQ ID NO: 762)CAGAGGAGAUAAAGAUGGAGAUAA CGCCAACCUGGCGGCAGCGCAAGA AG (SEQ ID NO: 752)32B_N1 GGGCUGGGAUCAAGUACAUGUAGU UUUUGCUCGUGGCGCACUACAUGUAGCGCCACGAGCAAAAGGACUUUAG CUUGAUCCCAG (SEQ ID NO: 763)AACAGAGGAGAUAAAGAUGUUUUG CUCGUGUAACCUGGCGGCAGCGCA AAAG (SEQ ID NO: 753)32B_N2 GGGCCUGCAGCCCUGGGAUCAAGU GGCGCACUACAUGUACUUGAUCCCAACAUGUAGUGCGCCGGACUUUAGA GGGCUGCAGGC (SEQ ID NO: 764)ACAGAGGAGAUAAAGAUGGGCGCA CUACAAACCUGGCGGCAGCGCAAG AAG (SEQ ID NO: 754)32B_N3 GGGCUGCCGUUCUCUUCUGGGCAG CAGCAGCUGCGCGUGCUGCCCAGAACACGCGCAGCUGCUGGGACUUUAG GAGAACGGCAG (SEQ ID NO: 765)AACAGAGGAGAUAAAGAUGCAGCA GCUGCGAACCUGGCGGCAGCGCAA GAAG (SEQ ID NO: 755)32B_N4 GGGCAGCCCUGGGAUCAAGUACAU CUCGUGGCGCACUACAUGUACUUGAGUAGUGCGCCACGAGGGACUUUAG UCCCAGGGCUG (SEQ ID NO: 766)AACAGAGGAGAUAAAGAUGCUCGU GGCGCAAACCUGGCGGCAGCGCAA GAAG (SEQ ID NO: 756)32B_N5 GGGAUGCCAGCUGCCGUUCUCUUC GCGCGUGCUGCCCAGAAGAGAACGGUGGGCAGCACGCGCGGACUUUAGA CAGCUGGCAUC (SEQ ID NO: 767)ACAGAGGAGAUAAAGAUGGCGCGU GCUGCAACCUGGCGGCAGCGCAAG AAG (SEQ ID NO: 757)

We claim:
 1. A method of detecting a target nucleic acid in a sample,the method comprising the steps of: (a) obtaining nucleic acid from abiological sample obtained from a subject; (b) amplifying the nucleicacid using isothermal amplification; (c) contacting the amplifiednucleic acid to a toehold switch, wherein the toehold switch encodes areporter protein and comprises one or more single-stranded toeholdsequence domains that are complementary to a target nucleic acid or thereverse complement thereof, wherein the contacting occurs underconditions that allow translation of the coding domain in the presenceof the target nucleic acid but not in the absence of the target nucleicacid, and detecting the reporter protein as an indicator that the targetnucleic acid is present in the amplified nucleic acid of the subject;and (d) identifying the target nucleic acid as containing a targetprotospacer adjacent motif (PAM), wherein identifying comprises: (i)amplifying nucleic acid obtained from the biological sample using areverse primer designed to append the trigger sequence of one or moretoehold switch sequence domains; (ii) contacting the amplified nucleicacid of (i) to CRISPR/Cas under conditions that allow forsequence-specific cleavage of the contacted nucleic acid by CRISPR/Caswhen the target PAM is present in the amplified nucleic acid; and (iii)detecting activation of the toehold switch, wherein activation does notoccur in the event of CRISPR/Cas-mediated sequence-specific cleavage,thereby indicating the presence of the target PAM.
 2. The method ofclaim 1, wherein the toehold switch comprises one or moresingle-stranded toehold sequence domains, a fully or partiallydouble-stranded stem domain comprising an initiation codon, a loopdomain comprising a ribosome binding site, and a coding domain.
 3. Themethod of claim 2, wherein the toehold and stem domains arecomplementary in sequence to a naturally occurring RNA.
 4. The method ofclaim 2, wherein the loop domain is complementary in sequence to anon-naturally occurring RNA.
 5. The method of claim 1, wherein thetarget nucleic acid is an RNA specific to a pathogen.
 6. The method ofclaim 1, wherein the pathogen is selected from the group consisting of avirus, bacterium, fungus, and parasite.
 7. The method of claim 1,wherein the isothermal amplification is selected from the groupconsisting of NASBA (nucleic acid sequence-based amplification),loop-mediated isothermal amplification (LAMP), recombinase polymeraseamplification (RPA), and helicase-dependent amplification (HAD).
 8. Themethod of claim 1, wherein the biological sample is selected from thegroup consisting of blood, serum, urine, saliva, tissue, cell, andorgan, or a fraction or portion thereof.
 9. A method of detecting atarget nucleic acid in a sample, the method comprising the steps of: (a)obtaining RNA from a biological sample obtained from a subject; (b)amplifying the RNA using isothermal amplification; (c) contacting theamplified RNA to a toehold switch, wherein the toehold switch encodes areporter protein and comprises one or more single-stranded toeholdsequence domains that are complementary to a target RNA or the reversecomplement thereof, wherein the contacting occurs under conditions thatallow translation of the coding domain in the presence of the target RNAbut not in the absence of the target RNA, and detecting the reporterprotein as an indicator that the target RNA is present in the amplifiedRNA of the subject; and (d) identifying the target RNA as containing atarget protospacer adjacent motif (PAM), wherein identifying comprises:(i) amplifying RNA obtained from the biological sample using a reverseprimer designed to append the trigger sequence of one or more toeholdswitch sequence domains; (ii) contacting the amplified RNA of (i) toCRISPR/Cas under conditions that allow for sequence-specific cleavage ofthe contacted RNA by CRISPR/Cas when the target PAM is present in theamplified RNA; and (iii) detecting activation of the toehold switch,wherein activation does not occur in the event of CRISPR/Cas-mediatedsequence-specific cleavage, thereby indicating the presence of thetarget RNA.
 10. The method of claim 9, wherein the toehold switchcomprises one or more single-stranded toehold sequence domains, a fullyor partially double-stranded stem domain comprising an initiation codon,a loop domain comprising a ribosome binding site, and a coding domain.11. The method of claim 10, wherein the toehold and stem domains arecomplementary in sequence to a naturally occurring RNA.
 12. The methodof claim 10, wherein the loop domain is complementary in sequence to anon-naturally occurring RNA.
 13. The method of claim 9, wherein thetarget nucleic acid is an RNA specific to a pathogen.